Article
Biochemical Research Methods
Deepshika Gilbile, Megan L. Shelby, Artem Y. Lyubimov, Jennifer L. Wierman, Diana C. F. Monteiro, Aina E. Cohen, Silvia Russi, Matthew A. Coleman, Matthias Frank, Tonya L. Kuhl
Summary: The development of versatile, inexpensive, and robust polymer microfluidic chips for serial X-ray crystallography allows for efficient sample delivery and measurements at both synchrotrons and X-ray free electron lasers. The chips offer advantages such as low sample consumption, minimal background scattering, and precise control over sample flow, making them suitable for a wide range of protein crystallography experiments.
Article
Biochemical Research Methods
Kevin K. Gu, Zhongrui Liu, Sankar Raju Narayanasamy, Megan L. Shelby, Nicholas Chan, Matthew A. Coleman, Matthias Frank, Tonya L. Kuhl
Summary: The development of X-ray free electron laser and continuous crystallography methodologies has revolutionized protein crystallography. The fixed-target system, utilizing microfluidic technology, has shown great potential in delivering difficult-to-handle microcrystals for serial crystallography measurements.
Article
Crystallography
Rafal Dolot, Anna Maciaszek, Barbara Mikolajczyk, Barbara Nawrot
Summary: The crystallization experiments of heteroduplexes composed of DNA and 2'-OMe RNA strands showed that overhangs at the ends of the duplex greatly influence the success of crystallization and the crystal packing. The structures of these heteroduplexes, which adopted a conformation close to the A-RNA double helix, provide insight into their properties and can be useful for future applications.
Article
Biochemistry & Molecular Biology
Christo N. Nanev, Emmanuel Saridakis, Naomi E. Chayen
Summary: X-ray crystallography is currently the dominant method for determining the structure of proteins and biomolecules. However, it faces challenges in obtaining high-resolution data from small protein crystals. Serial crystallography using XFELs is a promising alternative method that can produce excellent structural data from weakly diffracting objects. In this study, the authors calculate the mean crystal size and growth time needed for batch crystallization, which is the main method for preparing microcrystalline slurries. They also consider the impact of impurities on the growth of microcrystals. Experimental results with lysozyme support the theoretical predictions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Christopher J. Ohmer, Medhanjali Dasgupta, Anjali Patwardhan, Isabel Bogacz, Corey Kaminsky, Margaret D. Doyle, Percival Yang-Ting Chen, Stephen M. Keable, Hiroki Makita, Philipp S. Simon, Ramzi Massad, Thomas Fransson, Ruchira Chatterjee, Asmit Bhowmick, Daniel W. Paley, Nigel W. Moriarty, Aaron S. Brewster, Leland B. Gee, Roberto Alonso-Mori, Frank Moss, Franklin D. Fuller, Alexander Batyuk, Nicholas K. Sauter, Uwe Bergmann, Catherine L. Drennan, Vittal K. Yachandra, Junko Yano, Jan F. Kern, Stephen W. Ragsdale
Summary: Methyl-Coenzyme M Reductase (MCR) is a crucial enzyme in methanogenesis that has significant implications for global energy balances. However, the structure and reaction mechanism of this enzyme are still poorly understood.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Shuo Sui, Anne Mulichak, Raviraj Kulathila, Joshua McGee, Danny Filiatreault, Sarthak Saha, Aina Cohen, Jinhu Song, Holly Hung, Jonathan Selway, Christina Kirby, Om K. Shrestha, Wilhelm Weihofen, Michelle Fodor, Mei Xu, Rajiv Chopra, Sarah L. Perry
Summary: This novel approach utilizes capillary-based microfluidic devices and X-ray crystallography to accelerate the process of small-molecule-compound screening. The devices are designed for efficient sample manipulation and crystal handling, opening up new possibilities for research in this field.
JOURNAL OF APPLIED CRYSTALLOGRAPHY
(2021)
Article
Multidisciplinary Sciences
Akinobu Niozu, Yoshiaki Kumagai, Toshiyuki Nishiyama Hiraki, Hironobu Fukuzawa, Koji Motomura, Maximilian Bucher, Kazuki Asa, Yuhiro Sato, Yuta Ito, Daehyun You, Taishi Ono, Yiwen Li, Edwin Kukk, Catalin Miron, Liviu Neagu, Carlo Callegari, Michele Di Fraia, Giorgio Rossi, Davide Emilio Galli, Tommaso Pincelli, Alessandro Colombo, Shigeki Owada, Kensuke Tono, Takashi Kameshima, Yasumasa Joti, Tetsuo Katayama, Tadashi Togashi, Makina Yabashi, Kazuhiro Matsuda, Christoph Bostedt, Kiyoshi Ueda, Kiyonobu Nagaya
Summary: This study explores the formation process of solid Xe nanoparticles in an expanding supercooled Xe jet under vacuum conditions using X-ray diffraction experiments. It is found that the structure of Xe nanoparticles is a mixture of face-centered cubic and randomly stacked hexagonal close-packed structures, rather than pure face-centered cubic. Instantaneous coexistence of comparably sized face-centered cubic and hexagonal close-packed domains in single Xe nanoparticles is observed.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Physical
Cody Kunka, Apaar Shanker, Elton Y. Chen, Surya R. Kalidindi, Remi Dingreville
Summary: Traditional diffraction techniques are limited by the difficulty of decoding desired material information, but using machine learning and feature identification can more comprehensively and accurately predict structural information.
NPJ COMPUTATIONAL MATERIALS
(2021)
Article
Biochemistry & Molecular Biology
Supeshala Nawarathnage, Sara Soleimani, Moriah H. Mathis, Braydan D. Bezzant, Diana T. Ramirez, Parag Gajjar, Derick R. Bunn, Cameron Stewart, Tobin Smith, Maria J. Pedroza Romo, Seth Brown, Tzanko Doukov, James D. Moody
Summary: The study found that TELSAM-target protein fusions crystallize more rapidly and at lower protein concentrations compared to the target protein alone. TELSAM polymers do not need direct contact to form well-diffracting crystals. Fusion to TELSAM polymers can stabilize weak inter-target protein crystal contacts and adjust the helical rise of TELSAM polymers.
Article
Multidisciplinary Sciences
Linta M. Biju, Cong Wang, Weijia Kang, Irin P. Tom, Indika Kumarapperuma, Xiaojing Yang, Zhong Ren
Summary: This article introduces a powerful method for conducting X-ray diffraction experiments at room temperature, which allows for high-throughput processing of hundreds to thousands of protein crystals without sample manipulation.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2022)
Article
Multidisciplinary Sciences
Oliver F. Harder, Sarah V. Barrass, Marcel Drabbels, Ulrich J. Lorenz
Summary: Microsecond time-resolved cryo-EM allows for observation of fast protein dynamics, as demonstrated by the contraction of the CCMV capsid induced by a pH jump.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Fabrice Gorrec, Dom Bellini
Summary: The FUSION protein crystallization screen formulation is an innovative approach that integrates the most efficient components from three existing screens to produce high-quality crystals. It combines 96 unique combinations of crystallization additives, many of which are frequently found in crystal structures of proteins. The efficiency of FUSION is demonstrated by obtaining high yields of diffraction-quality crystals for seven different test proteins, including the discovery of two crystal forms not currently in the Protein Data Bank.
JOURNAL OF APPLIED CRYSTALLOGRAPHY
(2022)
Review
Chemistry, Multidisciplinary
Ha L. Nguyen
Summary: Reticular chemistry of covalent organic frameworks (COFs) focuses on linking discrete organic building units into extended structures through strong covalent bonds. Over the past decade, there has been rapid development in COF chemistry in terms of structural diversity and applications. Understanding the concept of reticular chemistry is essential for researching COFs and correlating their geometric structures and practical applications.
Article
Physics, Applied
Shigeru Sugiyama, Keisuke Kakinouchi, Hiroaki Adachi, Tsugio Nagasawa, Noriaki Kunimune, Michio Murata, Yusuke Mori
Summary: This study introduced a new method for protein crystallization in high-strength hydrogels to prevent protein damage at high temperatures and found that this method is applicable to various proteins due to its low-temperature operation.
JAPANESE JOURNAL OF APPLIED PHYSICS
(2021)
Article
Biochemical Research Methods
Dimitri Radajewski, Pierre Roblin, Patrice Bacchin, Martine Meireles, Yannick Hallez
Summary: Recent advances have enabled the integration of microfluidic chips with X-ray equipment for direct structural analysis of samples. Through improvements in X-ray laboratory beamline and microfluidic device design, reliable structural information can be obtained without the use of a synchrotron source.
Article
Multidisciplinary Sciences
Juraj Knoska, Luigi Adriano, Salah Awel, Kenneth R. Beyerlein, Oleksandr Yefanov, Dominik Oberthuer, Gisel E. Pena Murillo, Nils Roth, Iosifina Sarrou, Pablo Villanueva-Perez, Max O. Wiedorn, Fabian Wilde, Sasa Bajt, Henry N. Chapman, Michael Heymann
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
K. Libicher, R. Hornberger, M. Heymann, H. Mutschler
NATURE COMMUNICATIONS
(2020)
Article
Chemistry, Multidisciplinary
Jiaqing Wang, Weiyi Tan, Guanying Li, Difei Wu, Hongjian He, Jiashu Xu, Meihui Yi, Ye Zhang, S. Ali Aghvami, Seth Fraden, Bing Xu
CHEMISTRY-A EUROPEAN JOURNAL
(2020)
Article
Physics, Multidisciplinary
Michael M. Norton, Piyush Grover, Michael F. Hagan, Seth Fraden
PHYSICAL REVIEW LETTERS
(2020)
Article
Chemistry, Physical
James Sheehy, Ian Hunter, Maria Eleni Moustaka, S. Ali Aghvami, Youssef Fahmy, Seth Fraden
JOURNAL OF PHYSICAL CHEMISTRY B
(2020)
Article
Chemistry, Physical
Theodore Lupinski, Markus Ludwig, Seth Fraden, Nathan Tompkins
Summary: Constant pressure pumps play a crucial role in microfluidic flow systems, stabilizing fluid pressure and adapting to systems requiring pressure stability. These pumps are cost-effective and suitable for use in undergraduate institutions and laboratories with limited research budgets.
EUROPEAN PHYSICAL JOURNAL E
(2021)
Article
Chemistry, Multidisciplinary
Sarah E. Zuraw-Weston, Mahsa Siavashpouri, Maria E. Moustaka, Thomas Gerling, Hendrik Dietz, Seth Fraden, Alexander E. Ribbe, Anthony D. Dinsmore
Summary: This experimental study explores the impact of nanorods binding to lipid bilayer vesicles and altering membrane shape. By adjusting adhesion strength, membrane tension, and particle concentration, it was found that increasing adhesion strength led to membrane deformation, vesicle-vesicle adhesion, and vesicle rupture. These findings provide insight into the physical mechanisms behind membrane remodeling and may inspire the development of new bioinspired materials.
Article
Chemistry, Physical
Maria Eleni Moustaka, Michael M. Norton, Baptiste Blanc, Viktor Horvath, S. Ali Aghvami, Seth Fraden
Summary: Experiments and models were used to investigate the permeation and reaction of aqueous bromine in PDMS, revealing the diffusion, reversible binding, and irreversible reaction processes between bromine and PDMS.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Physical
Christian Sigl, Elena M. Willner, Wouter Engelen, Jessica A. Kretzmann, Ken Sachenbacher, Anna Liedl, Fenna Kolbe, Florian Wilsch, S. Ali Aghvami, Ulrike Protzer, Michael F. Hagan, Seth Fraden, Hendrik Dietz
Summary: This study introduces a programmable icosahedral canvas for the self-assembly of icosahedral shells with viral trapping and antiviral properties. It demonstrates the potential of a new broad-spectrum antiviral platform that could alleviate many threats to global public health.
Article
Multidisciplinary Sciences
Kristian Thijssen, Dimitrius A. Khaladj, S. Ali Aghvami, Mohamed Amine Gharbi, Seth Fraden, Julia M. Yeomans, Linda S. Hirst, Tyler N. Shendruk
Summary: The coupling between flows and material properties makes rheological matter widely applicable, and the study proposes a method for controlling flow, topology, and composition within active films by using micropatterned structures within an underlying oil layer to establish rheological coupling.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Physics, Multidisciplinary
Linnea M. Lemma, Michael M. Norton, Alexandra M. Tayar, Stephen J. DeCamp, S. Ali Aghvami, Seth Fraden, Michael F. Hagan, Zvonimir Dogic
Summary: The study quantified the motion of microtubule bundles, revealing that the extension speed of isolated bundles is faster than that in dense active nematics. In the dense active nematic, the sliding speeds of filaments are widely distributed, showing both contractile and extensile relative motion.
PHYSICAL REVIEW LETTERS
(2021)
Article
Multidisciplinary Sciences
John Berezney, Bruce L. Goode, Seth Fraden, Zvonimir Dogic
Summary: This study investigates a reconstituted composite system composed of an active microtubule network and a passive F-actin filament network. By increasing the concentration of actin filaments, the system's dynamics transition from turbulent-like flows to bulk contractions. At intermediate concentrations, the composite separates into layered asters that coexist with a background turbulent fluid. These structures self-organize and have a defined lifetime.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Proceedings Paper
Materials Science, Multidisciplinary
U. Hommerich, J. Barnett, A. Kabir, K. Ghebreyessus, K. Hampton, S. Uba, I Uba, D. Geddis, C. Yang, S. Trivedi, S. Fraden, Ali Aghvami
Summary: Manganese doped CsPbCl3 bulk crystals and nanoparticles were prepared and their emission properties were compared in this study. The results showed significant differences in excitation spectra, emission characteristics, and emission lifetimes between the two forms.
OPTICAL COMPONENTS AND MATERIALS XVIII
(2021)
Article
Physics, Fluids & Plasmas
Yi Fan, Kun-Ta Wu, S. Ali Aghvami, Seth Fraden, Kenneth S. Breuer
Summary: This study investigates the dynamics and structure of kinesin-driven microtubule active fluids as the height of the container increases. The activity level, characterized by velocity fluctuations, increases with system size while maintaining small-scale isotropy. The velocity-velocity temporal correlation develops a strong positive correlation at longer times as the confinement level decreases.
Article
Chemistry, Physical
Zhengyang Zhou, Chaitanya Joshi, Ruoshi Liu, Michael M. Norton, Linnea Lemma, Zvonimir Dogic, Michael F. Hagan, Seth Fraden, Pengyu Hong
Summary: Active nematics are materials characterized by local orientational order and anisotropic constitutes of force generation, usually studied using traditional hydrodynamic models. Researchers have developed a deep learning approach using ConvLSTM algorithm to predict the dynamics of active nematics, regardless of traditional models.