Article
Chemistry, Multidisciplinary
Leonhard H. Urner, Katharina Goltsche, Marleen Selent, Idlir Liko, Marc-Philip Schweder, Carol Robinson, Kevin Pagel, Rainer Haag
Summary: Dendrons, an important class of macromolecules, have been found to be more effective for protein extraction when using mixtures of oligoglycerol detergent regioisomers than individual regioisomers. The synthesis and characterization of these mixtures, along with their implementation into detergents, have been discussed, with experimental benchmarks provided for quality control. The unusual utility of these mixtures for extracting large protein quantities from biological membranes is investigated, with the anticipation that these findings will contribute to the development of mixed detergent platforms in the future.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Weiling Luo, Meifang Yang, Yitian Zhao, Huixia Wang, Xiaodi Yang, Wei Zhang, Fei Zhao, Suwen Zhao, Houchao Tao
Summary: This study presents the design of novel detergents with a transition linker for gradual change of hydrophobicity. These detergents form micelles with low critical micelle concentrations and exhibit superior thermal stabilizing properties for membrane proteins. The results suggest potential for expanding the application of detergents through remodeling of traditional detergent scaffold.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Physical
Sanghamitra Sengupta, Rahul Gera, Colin Egan, Uriel N. Morzan, Jan Versluis, Ali Hassanali, Huib J. Bakker
Summary: The interfacial vibrational footprints of SDS and C12E6 binary mixture were investigated using HDVSFG. The presence of C12E6 enhances the effect of SDS on the orientation of interfacial water molecules, contrary to the predictions of the traditional Langmuir adsorption model. Molecular dynamics simulations also support this observation.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Multidisciplinary
Kyle A. Brown, Morgan K. Gugger, David S. Roberts, David Moreno, Pil Seok Chae, Ying Ge, Song Jin
Summary: We synthesized and characterized a new family of maltose-derived nonionic surfactants containing a photocleavable azo-sulfide linker (mAzo). The self-assembly properties of these surfactants were studied using various techniques, including surface tension measurements, dynamic light scattering, and transmission electron microscopy. The photodegradation process of these surfactants was investigated, revealing the formation of a photo-stable surfactant post-degradation. Furthermore, these mAzo surfactants demonstrated potential in solubilizing challenging proteins from heart tissue.
Article
Biochemistry & Molecular Biology
Alexia Gobet, Veronica Zampieri, Sandrine Magnard, Eva Pebay-Peyroula, Pierre Falson, Vincent Chaptal
Summary: Concentration of pure membrane proteins in detergent solution leads to an increase in detergent concentration, the exact amount of which is unknown. Although commonly observed in membrane protein research labs, this phenomenon has been rarely investigated. In this study, we examined the behavior of detergents mixed with membrane proteins during sample concentration using centrifugal devices. We found that the presence of polymers, including membrane or soluble proteins and polysaccharides, results in detergent over-concentration. The degree of detergent over-concentration depends on the centrifugal force applied. By using a specific dye, we observed the formation of a mesh on the concentrator device. Importantly, reducing the centrifugal speed helps decrease the detergent concentration when mixed with macromolecules, as demonstrated with three different membrane proteins. Overall, these findings highlight the non-Newtonian behavior of detergents and provide a valuable framework for improving biochemical and structural studies of membrane proteins.
Article
Biochemistry & Molecular Biology
Taeyeol Youn, Soyoung Yoon, Bernadette Byrne, Pil Seok Chae
Summary: Detergents with multiple tail and head groups have been widely used for structural studies of membrane proteins. Recent research has shown that these detergents, despite having large inter-alkyl chain distances, can effectively stabilize membrane proteins. This is achieved by incorporating a flexible spacer between two triazine rings in the detergent's linker region, allowing it to fold into a compact architecture in micellar environments. The foldability of detergents represents a new concept for detergent design and has significant potential for future development.
Article
Biochemical Research Methods
J. Barroca-Ferreira, A. M. Goncalves, M. F. A. Santos, T. Santos-Silva, C. J. Maia, L. A. Passarinha
Summary: STEAP1 is an integral membrane protein that is over-expressed in prostate cancer and plays a role in cellular communications, cell proliferation, and transmembrane-electron transport. In this study, the recombinant protein rhSTEAP1-His6 was successfully expressed and purified, providing a foundation for further investigations into its structural and functional roles.
JOURNAL OF CHROMATOGRAPHY A
(2022)
Article
Biochemistry & Molecular Biology
Dane Sands, Andrew Davis, Scott Banfield, Ian R. Pottie, Sultan Darvesh
Summary: Acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) are enzymes with various physiological functions. Inhibitors for these enzymes, which have low aqueous solubility, have been studied for the treatment of different conditions. This study evaluated the effects of cosolvents and detergents on cholinesterase activity, and found that propylene glycol, acetonitrile, methanol, Tween 20, Polysorbate 80 (Tween 80), polyoxyethylene 23 lauryl ether (Brij 35), and polyoxyethylene 10 oleoyl ether (Brij 96v) had the least inhibitory effects. These solubilizing agents can be considered for evaluating potential cholinesterase inhibitors with low aqueous solubility.
CHEMICO-BIOLOGICAL INTERACTIONS
(2023)
Article
Immunology
Yun Lu, Xinxin Hu, Tongying Nie, Xinyi Yang, Congran Li, Xuefu You
Summary: Study on the membrane proteome of Acinetobacter baumannii revealed a rapid and effective preparation method, providing a more comprehensive view of changes in the membrane proteome under polymyxin B pressure.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
William Godefroy, Lionel Faivre, Caroline Sansac, Briac Thierry, Jean-Marc Allain, Patrick Bruneval, Remy Agniel, Sabrina Kellouche, Olivier Monasson, Elisa Peroni, Mohamed Jarraya, Niclas Setterblad, Massymissa Braik, Benjamin Even, Sophie Cheverry, Thomas Domet, Patricia Albanese, Jerome Larghero, Pierre Cattan, Lousineh Arakelian
Summary: We have successfully developed a clinical grade decellularized and cryopreserved human esophagus using sodium dodecyl sulfate and ethylendiaminetetraacetic acid for decellularization and a safe cryopreservation protocol. The structure and biomechanical properties of the esophagus were preserved.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Yoonji Bae, Sang Kwon Lee, Young Chan Chae, Chan Young Park, Sebyung Kang
Summary: Covalent protein-ligation methods were used to visualize the localization of proteins in cells and study the topology of membrane proteins. By selectively labeling membrane proteins in a topology-dependent manner, the method proved to be effective in both live and permeabilized cells.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Review
Biophysics
Christel Le Bon, Baptiste Michon, Jean-Luc Popot, Manuela Zoonens
Summary: In the past decade, membrane protein structural biology has advanced thanks to the breakthrough in single-particle cryo-EM technology and improvements in sample preparation, with various surfactants being extensively used and optimized for studies. The diversity in surfactant choices and experimental approaches underscores the ongoing need for developing innovative surfactants and refining sample preparation conditions in the field of cryo-EM research.
QUARTERLY REVIEWS OF BIOPHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Amanda C. Carita, Rafaela R. M. Cavalcanti, Mariana S. S. Oliveira, Karin A. Riske
Summary: This study investigates the solubilization of lipid vesicles by various non-ionic detergents and compares the results with a standard detergent. The results show that only TX-100 and OG are able to completely solubilize the vesicles.
CHEMISTRY AND PHYSICS OF LIPIDS
(2023)
Article
Chemistry, Multidisciplinary
Fei Zhao, Zhihao Zhu, Linshan Xie, Feng Luo, Huixia Wang, Yanli Qiu, Weiling Luo, Fang Zhou, Dongxiang Xue, Zhihui Zhang, Tian Hua, Dong Wu, Zhi-Jie Liu, Zhiping Le, Houchao Tao
Summary: Detergents are commonly used in membrane protein studies, but the limited diversity of traditional detergents restricts their applications to structurally distinct proteins. In this study, the authors report the cross-conjugation of two series of monomeric detergents to construct a library of dimeric detergents for a wider range of applications. Optimum detergents were identified through systematic evaluation and hybrid detergents enabled high-quality studies of different proteins. The findings suggest that the use of cross-coupling chemistries can greatly expand the diversity of detergents for future studies on membrane proteins.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Multidisciplinary Sciences
Yuzuru Itoh, Juni Andrell, Austin Choi, Uwe Richter, Priyanka Maiti, Robert B. Best, Antoni Barrientos, Brendan J. Battersby, Alexey Amunts
Summary: The study reveals the mechanism of interaction between human mitoribosomes and the insertase OXA1L, elucidating how membrane delivery is achieved during protein synthesis.
Article
Biochemistry & Molecular Biology
Martin Audet, Kate L. White, Billy Breton, Barbara Zarzycka, Gye Won Han, Yan Lu, Cornelius Gati, Alexander Batyuk, Petr Popov, Jeffrey Velasquez, David Manahan, Hao Hu, Uwe Weierstall, Wei Liu, Wenqing Shui, Vsevolod Katritch, Vadim Cherezov, Michael A. Hanson, Raymond C. Stevens
NATURE CHEMICAL BIOLOGY
(2019)
Correction
Biochemistry & Molecular Biology
Martin Audet, Kate L. White, Billy Breton, Barbara Zarzycka, Gye Won Han, Yan Lu, Cornelius Gati, Alexander Batyuk, Petr Popov, Jeffrey Velasquez, David Manahan, Hao Hu, Uwe Weierstall, Wei Liu, Wenqing Shui, Vsevolod Katritch, Vadim Cherezov, Michael A. Hanson, Raymond C. Stevens
NATURE CHEMICAL BIOLOGY
(2019)
Article
Biochemical Research Methods
Christian Munk, Eshita Mutt, Vignir Isberg, Louise F. Nikolajsen, Janne M. Bibbe, Tilman Flock, Michael A. Hanson, Raymond C. Stevens, Xavier Deupi, David E. Gloriam
Article
Multidisciplinary Sciences
Shuanghong Chen, Mengjie Lu, Dongsheng Liu, Lingyun Yang, Cuiying Yi, Limin Ma, Hui Zhang, Qing Liu, Thomas M. Frimurer, Ming-Wei Wang, Thue W. Schwartz, Raymond C. Stevens, Beili Wu, Kurt Wuthrich, Qiang Zhao
NATURE COMMUNICATIONS
(2019)
Article
Chemistry, Analytical
Yan Lu, Shanshan Qin, Bingjie Zhang, Antao Dai, Xiaoqing Cai, Mengna Ma, Zhan-Guo Gao, Dehua Yang, Raymond C. Stevens, Kenneth A. Jacobson, Ming-Wei Wang, Wenqing Shui
ANALYTICAL CHEMISTRY
(2019)
Article
Multidisciplinary Sciences
Linda C. Johansson, Benjamin Stauch, John D. McCorvy, Gye Won Han, Nilkanth Patel, Xi-Ping Huang, Alexander Batyuk, Cornelius Gati, Samuel T. Slocum, Chufeng Li, Jessica M. Grandner, Shuming Hao, Reid H. J. Olsen, Alexandra R. Tribo, Sahba Zaare, Lan Zhu, Nadia A. Zatsepin, Uwe Weierstall, Said Yous, Raymond C. Stevens, Wei Liu, Bryan L. Roth, Vsevolod Katritch, Vadim Cherezov
Article
Multidisciplinary Sciences
Benjamin Stauch, Linda C. Johansson, John D. McCorvy, Nilkanth Patel, Gye Won Han, Xi-Ping Huang, Cornelius Gati, Alexander Batyuk, Samuel T. Slocum, Andrii Ishchenko, Wolfgang Brehm, Thomas A. White, Nairie Michaelian, Caleb Madsen, Lan Zhu, Thomas D. Grant, Jessica M. Grandner, Anna Shiriaeva, Reid H. J. Olsen, Alexandra R. Tribo, Said Yous, Raymond C. Stevens, Uwe Weierstall, Vsevolod Katritch, Bryan L. Roth, Wei Liu, Vadim Cherezov
Correction
Multidisciplinary Sciences
Benjamin Stauch, Linda C. Johansson, John D. McCorvy, Nilkanth Patel, Gye Won Han, Xi-Ping Huang, Cornelius Gati, Alexander Batyuk, Samuel T. Slocum, Andrii Ishchenko, Wolfgang Brehm, Thomas A. White, Nairie Michaelian, Caleb Madsen, Lan Zhu, Thomas D. Grant, Jessica M. Grandner, Anna Shiriaeva, Reid H. J. Olsen, Alexandra R. Tribo, Said Yous, Raymond C. Stevens, Uwe Weierstall, Vsevolod Katritch, Bryan L. Roth, Wei Liu, Vadim Cherezov
Article
Biochemistry & Molecular Biology
Jack C. Li, Fariborz Nastertorabi, Weimin Xuan, Gye Won Han, Raymond C. Stevens, Peter G. Schultz
ACS CHEMICAL BIOLOGY
(2019)
Article
Biochemical Research Methods
Martin Audet, Kelly Villers, Jeffrey Velasquez, Meihua Chu, Chris Hanson, Raymond C. Stevens
Article
Multidisciplinary Sciences
Xianjun Zhang, Stephen D. Carter, Jitin Singla, Kate L. White, Peter C. Butler, Raymond C. Stevens, Grant J. Jensen
Article
Biochemistry & Molecular Biology
Jitin Singla, Kate L. White, Raymond C. Stevens, Frank Alber
Summary: Cryo-electron tomography allows for unsupervised discovery of endogenous complexes, but assessing the quality of aligned subtomogram clusters with scoring functions can be sensitive to signal-to-noise ratio. Spectral SNR-based Fourier Shell Correlation and Pearson Correlation are robust scoring functions for template-free clustering, with the former being faster for handling large numbers of subtomograms.
JOURNAL OF STRUCTURAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jitin Singla, Kylie Burdsall, Brian Cantrell, Jordan R. Halsey, Alex McDowell, Colleen McGregor, Sanraj Mittal, Raymond C. Stevens, Shaoyu Su, Alexandra Thomopoulos, Theotime Vaillant, Kate L. White, Bryan Zhang, Helen M. Berman
Summary: As part of a project, a spatiotemporal model of the pancreatic b-cell is being built and an immersive experience called World in a Cell is being created for integrating and generating new educational tools. A new visual design language using tetrahedral building blocks has been developed to represent the structural features of biological molecules and organelles in crowded cellular environments, enabling more efficient animation and user interaction in the immersive environment.
Article
Chemistry, Organic
Dongxiang Xue, Lintao Ye, Jun Zheng, Yiran Wu, Xianjun Zhang, Yueming Xu, Tao Li, Raymond C. Stevens, Fei Xu, Min Zhuang, Suwen Zhao, Fei Zhao, Houchao Tao
ORGANIC & BIOMOLECULAR CHEMISTRY
(2019)
Article
Chemistry, Multidisciplinary
M. Gertrude Gutierrez, Jacob Deyell, Kate L. White, Lucia C. Dalle Ore, Vadim Cherezov, Raymond C. Stevens, Noah Malmstadt
CHEMICAL COMMUNICATIONS
(2019)