Article
Multidisciplinary Sciences
Sanjoy Paul, Anjon Audhya, Qiang Cui
Summary: The Sar1 GTPase plays a key role in COPII-mediated protein transport by generating membrane curvature on the endoplasmic reticulum. However, the molecular mechanism by which Sar1 is activated and regulates membrane remodeling remains unclear. Using molecular dynamics simulations, we show that Sar1-GTP inserts into the membrane more efficiently and generates higher positive curvature compared to Sar1-GDP. Dimerization of Sar1-GTP further amplifies curvature generation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Multidisciplinary
Xiangyang Guo, Jan Steinkuehler, Mariana Marin, Xiang Li, Wuyuan Lu, Rumiana Dimova, Gregory B. Melikyan
Summary: IFITM3 inhibits the transition from hemifusion to full fusion by inducing negative membrane curvature and increasing membrane order and stiffness, thus blocking the entry of diverse enveloped viruses.
Article
Chemistry, Multidisciplinary
Hyun-Soo Kim, Yeongju Lee, Min Hyeon Shin, Hyun-Suk Lim
Summary: The study describes the design, synthesis, and biological evaluation of cell-penetrating, amphipathic cyclic peptoids as an innovative class of molecular transporters. The cyclic peptoids show significantly improved intracellular delivery capability compared to traditional polyarginine cell-penetrating peptides, making them one of the best molecular transporters reported to date. With excellent cell-permeability, proteolytic stability, and ease of synthesis, the amphipathic cyclic peptoids have broad potential for clinical and biological applications.
CHEMICAL COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Anais Vlieghe, Kristina Niort, Hugo Fumat, Jean-Michel Guigner, Mickael M. Cohen, David Tareste
Summary: Mitochondrial fusion is crucial for maintaining the shape, distribution, and function of mitochondria. This study found that phosphatidylethanolamine (PE) and phosphatidic acid (PA) in the mitochondrial membrane effectively stimulate fusion, while cardiolipin (CL) has a slight inhibitory effect. The interplay between divalent cations and specific cone-shaped lipids creates a favorable environment for fusion.
Article
Multidisciplinary Sciences
Akimitsu Higuchi, Wataru Shihoya, Masae Konno, Tatsuya Ikuta, Hideki Kandori, Keiichi Inoue, Osamu Nureki
Summary: SzRs, a newly identified rhodopsin family in Asgard archaea, exhibit unique kinetic behaviors in inward H+ release compared to other H+ pumps. The crystal structure of SzR AM_5_00977 revealed that key residues and structural features are different from other microbial rhodopsins, suggesting a distinct mechanism for inward H+ release.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Multidisciplinary
Cen Chen, Ziyuan Fang, Zhen Huang
Summary: Crystallization phasing and obtaining high-quality crystals are major challenges for X-ray crystallographic analysis of nucleic acids. In this study, the authors addressed these challenges by incorporating selenium atoms into DNA duplexes, which resulted in larger and higher quality crystals compared to standard DNA crystals. These findings provide a simple strategy to overcome crystallization challenges in nucleic acid crystallography.
CRYSTAL GROWTH & DESIGN
(2022)
Article
Biology
Hai Li, Chia-Ying Huang, Elena G. Govorunova, Oleg A. Sineshchekov, Adrian Yi, Kenneth J. Rothschild, Meitian Wang, Lei Zheng, John L. Spudich
Summary: The crystal structure of bromide-bound GtACR1 reveals structural changes that relax the constrictions of the channel and involve a novel salt-bridge switch mechanism. These findings suggest that substrate binding induces a transition from an inactivated state to a pre-activated state in the dark, facilitating channel opening.
Article
Biochemistry & Molecular Biology
Satchal K. Erramilli, Pawel K. Dominik, Dawid Deneka, Piotr Tokarz, Sangwoo S. Kim, Bharat G. Reddy, Blazej M. Skrobek, Olivier Dalmas, Eduardo Perozo, Anthony A. Kossiakoff
Summary: CorA is a primary magnesium ion channel in prokaryotes and archaea. Synthetic antibodies (sABs) against CorA were generated using phage display selection strategies, and they showed different degrees of Mg2+-sensitivity. The sABs provided insights into the binding mode and mechanism of action of CorA.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Chemistry, Physical
Matthew N. Podgorski, Joshua S. Harbort, Joel H. Z. Lee, Giang T. H. Nguyen, John B. Bruning, William A. Donald, Paul Bernhardt, Jeffrey R. Harmer, Stephen G. Bell
Summary: In this study, it was found that mutating a highly conserved threonine residue in CYP199A4 to glutamate can convert it to a peroxygenase and improve its peroxygenase activity. The crystal structure of the mutant demonstrated a change in spin state upon substrate binding, which was linked to the modification of the oxygen-binding groove and the retention of the iron-bound aqua ligand. The detailed characterization of this engineered heme peroxygenase will aid in the development of new methods for the selective C-H bond activation using heme enzymes.
Article
Chemistry, Multidisciplinary
Jiali Yang, Takahiro Mori, Xingxing Wei, Yudai Matsuda, Ikuro Abe
Summary: The novel isomerase NsrQ from Aspergillus novofumigatus plays a key role in the biosynthesis of fungal tetrahydroxanthones by catalyzing a two-step isomerization reaction. Through biochemical and structural characterizations, it was found that NsrQ and its homologue Dcr3 utilize Glu and His residues as acid-base catalysts and important hydrophobic residues for shaping the active site pocket for substrate binding. The crystal structures of NsrQ and Dcr3 revealed their cone-shaped alpha + beta barrel fold and similarities to the nuclear transport factor 2-like superfamily enzymes.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Filip Topic, Joseph M. Marrett, Tristan H. Borchers, Hatem M. Titi, Christopher J. Barrett, Tomislav Friscic
Summary: This study presents the first X-ray single crystal structures of hypochlorite and hypobromite salts, shedding light on the solid-state geometry and supramolecular chemistry of hypohalite ions through variable-temperature Raman spectroscopy and periodic density-functional theory calculations.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
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
Biochemistry & Molecular Biology
Sunbin Deng, Jiaxi Cai, Stephen C. Harrison, Huilin Zhou, Stephen M. Hinshaw
Summary: Successful mitosis relies on the correct attachment of chromosomes to microtubules. The kinetochore plays a crucial role in this process by recognizing specific chromatin and ensuring the formation of only one kinetochore per chromatid at the correct location. The crystal structure of the Cse4 peptide bound to the inner kinetochore Okp1-Ame1 complex provides insights into centromere recognition and the organization of the inner kinetochore.
Article
Biochemistry & Molecular Biology
Hetao Chen, Hang Zhang, Pu Chen, Song Xiang
Summary: This study elucidated the interaction mechanism between CRTCs and 14-3-3, as well as their crucial roles in nuclear translocation and activation of gene transcription. The discovery of a novel salt bridge structure expanded the understanding of this interaction.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Physics, Applied
Jong Woo Kim, Mathew J. Cherukara, Ashish Tripathi, Zhang Jiang, Jin Wang
Summary: Coherent surface scattering imaging requires a mathematical conversion to visualize specimen structures, which can now be predicted using a deep learning neural network model to instantly obtain results from scattering patterns. This is highly beneficial for both experimental effectiveness and data analysis.
APPLIED PHYSICS LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Frank Jaenecke, Beatrice Friedrich-Epler, Christoph Parthier, Milton T. Stubbs
Article
Biochemistry & Molecular Biology
Stephan Zimmermann, Sabrina Pfennig, Piotr Neumann, Huma Yonus, Ulrich Weininger, Michael Kovermann, Jochen Balbach, Milton T. Stubbs
Article
Biochemistry & Molecular Biology
Hendrik Osadnik, Michael Schoepfel, Eyleen Heidrich, Denise Mehner, Hauke Lilie, Christoph Parthier, H. Jelger Risselada, Helmut Grubmueller, Milton T. Stubbs, Thomas Brueser
MOLECULAR MICROBIOLOGY
(2015)
Article
Biochemistry & Molecular Biology
Anke Piechotta, Christoph Parthier, Martin Kleinschmidt, Kathrin Gnoth, Thierry Pillot, Inge Lues, Hans-Ulrich Demuth, Stephan Schilling, Jens-Ulrich Rahfeld, Milton T. Stubbs
JOURNAL OF BIOLOGICAL CHEMISTRY
(2017)
Article
Biochemical Research Methods
Kumar Nagarathinam, Frank Jaenecke, Yoshiko Nakada-Nakura, Yunhon Hotta, Kehong Liu, So Iwata, Milton T. Stubbs, Norimichi Nomura, Mikio Tanabe
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2017)
Article
Chemistry, Multidisciplinary
Camila A. Cotrim, Annett Weidner, Nadine Strehmel, Tula B. Bisol, Danilo Meyer, Wolfgang Brandt, Ludger A. Wessjohann, Milton T. Stubbs
Article
Chemistry, Multidisciplinary
Sandra Liebscher, Michael Schoepfel, Tobias Aumueller, Ariunkhur Sharkhuukhen, Andreas Pech, Eva Hoess, Christoph Parthier, Guenther Jahreis, Milton T. Stubbs, Frank Bordusa
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2014)
Editorial Material
Biochemistry & Molecular Biology
Milton T. Stubbs, Elmar Wahle
Article
Biochemistry & Molecular Biology
Claudia Simon, Thomas Klose, Sabine Herbst, Bong Gyoon Han, Andrea Sinz, Robert M. Glaeser, Milton T. Stubbs, Hauke Lilie
JOURNAL OF BIOLOGICAL CHEMISTRY
(2014)
Article
Multidisciplinary Sciences
Christoph Parthier, Marco Stelter, Christian Ursel, Uwe Fandrich, Hauke Lilie, Constanze Breithaupt, Milton T. Stubbs
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2014)
Article
Multidisciplinary Sciences
Kumar Nagarathinam, Yoshiko Nakada-Nakura, Christoph Parthier, Tohru Terada, Narinobu Juge, Frank Jaenecke, Kehong Liu, Yunhon Hotta, Takaaki Miyaji, Hiroshi Omote, So Lwata, Norimichi Nomura, Milton T. Stubbs, Mikio Tanabe
NATURE COMMUNICATIONS
(2018)
Article
Multidisciplinary Sciences
Farzad Hamdi, Christian Tueting, Dmitry A. Semchonok, Koen M. Visscher, Fotis L. Kyrilis, Annette Meister, Ioannis Skalidis, Lisa Schmidt, Christoph Parthier, Milton T. Stubbs, Panagiotis L. Kastritis
Article
Biochemistry & Molecular Biology
Nadine Taudte, Miriam Linnert, Jens-Ulrich Rahfeld, Anke Piechotta, Daniel Ramsbeck, Mirko Buchholz, Petr Kolenko, Christoph Parthier, John A. Houston, Florian Veillard, Sigrun Eick, Jan Potempa, Stephan Schilling, Hans-Ulrich Demuth, Milton T. Stubbs
Summary: The research suggests that oral pathogen QCs could be potential target enzymes for small-molecule inhibitor development, with differences from animal QCs possibly aiding in the development of selective inhibitors. Recombinantly expressed QCs exhibit high catalytic efficiency and are inhibited by metal chelators. Significant differences around the active site of bacteroidal QCs compared to animal enzymes may help in the development of highly specific bacteroidal QC inhibitors.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Archna Prasad, Constanze Breithaupt, Duc-Anh Nguyen, Hauke Lilie, Joerg Ziegler, Milton T. Stubbs
Summary: This study presents crystal structures of MqnA protein and its active site mutants, revealing its important role in the biosynthesis pathway of vitamin K2.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Editorial Material
Multidisciplinary Sciences
Jochen Balbach, Milton T. Stubbs
Summary: Phage protein E kills bacteria by shutting down cell wall biosynthesis.