Article
Physiology
Youbin Zhang, Tianquan Jin, Weiying Zhu, Mirali Pandya, Gokul Gopinathan, Michael Allen, David Reed, Timothy Keiderling, Xiubei Liao, Thomas G. H. Diekwisch
Summary: This study reveals the intimate relationship between enamel matrix pH, enamel protein self-assembly, and enamel crystal growth. The highly acidic pH of the early enamel matrix is shown to be essential for enamel protein structure and self-assembly, apatite crystal growth, and protein interactions.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Cayla A. Stifler, Hajime Yamazaki, Pupa U. P. A. Gilbert, Henry C. Margolis, Elia Beniash
Summary: Amelogenin phosphorylation plays crucial roles in controlling the structural, crystallographic, mechanical, and compositional characteristics of dental enamel.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sarah M. Smith, Gabrielle Larocque, Katherine M. Wood, Kyle L. Morris, Alan M. Roseman, Richard B. Sessions, Stephen J. Royle, Corinne J. Smith
Summary: The interaction between Clathrin and the AP2 complex plays a crucial role in coated-pit assembly, with a beta 2 appendage able to bind in at least two positions in the clathrin cage. This multi-modal binding is shown to be a fundamental property of clathrin-AP2 interactions.
Article
Biochemistry & Molecular Biology
Alexander L. Danesi, Dimitra Athanasiadou, Ahmad Mansouri, Alina Phen, Mehrnoosh Neshatian, James Holcroft, Johan Bonde, Bernhard Ganss, Karina M. M. Carneiro
Summary: Biomineralization is a crucial process in which organisms produce mineralized tissues, such as teeth, bones, and shells, composed of hierarchically organized hydroxyapatite crystals. Developing protein-based materials as artificial scaffolds for guiding hydroxyapatite growth is an attractive goal for designing ordered nanomaterials and tissue regeneration. Uniaxial hydroxyapatite growth on a nanoengineered amelogenin scaffold combined with amelotin may provide insights into the molecular mechanism of hydroxyapatite formation and mineralized tissue formation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Cell Biology
Helena M. Schnell, Richard M. Walsh, Shaun Rawson, John Hanna
Summary: Cellular activities are often mediated by large multisubunit complexes, which require dedicated chaperone proteins for biogenesis. The proteasome, a crucial cellular regulator, consists of core particle and regulatory particle. The biogenesis pathway of CP involves a multistep process with the assistance of specific chaperones.
JOURNAL OF CELL SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Xiangwen Wang, Yonggang Lu, Xianghong Lin, Jianwei Li, Zequn Zhang
Summary: This paper proposes an unsupervised heterogeneous cryo-EM projection image classification algorithm based on autoencoders, which can effectively extract category features of heterogeneous projection images and achieve high classification and reconstruction accuracy, making it effective for heterogeneous 3D reconstruction in single-particle cryo-EM.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Yibo Jin, Paul K. Fyfe, Scott Gardner, Stephan Wilmes, Doryen Bubeck, Ignacio Moraga
Summary: IL-27 is an important cytokine that induces immunosuppressive responses. The study reveals the structure of the IL-27 receptor recognition complex and provides insights into the mechanism of IL-27 signaling. These findings contribute to a better understanding of IL-27's function and regulation.
Article
Engineering, Electrical & Electronic
Harshit Gupta, Michael T. McCann, Laurene Donati, Michael Unser
Summary: CryoGAN is a new paradigm for single-particle cryo-electron microscopy reconstruction based on unsupervised deep adversarial learning, achieving 3D structure reconstruction via distribution matching and skipping pose estimation or marginalization. It has shown success in recovering correct structures in an idealized mathematical model and achieving 10.8 angstrom resolution on a realistic synthetic dataset.
IEEE TRANSACTIONS ON COMPUTATIONAL IMAGING
(2021)
Article
Chemistry, Multidisciplinary
Dari Kimanius, Gustav Zickert, Takanori Nakane, Jonas Adler, Sebastian Lunz, Carola-Bibiane Schonlieb, Ozan Oktem, Sjors H. W. Scheres
Summary: This paper introduces a regularization framework for cryo-EM structure determination that utilizes prior knowledge about biological structures through a convolutional neural network trained on known macromolecular structures. The method yields better reconstructions than current state-of-the-art techniques for simulated data, and possibilities for extending this work to experimental cryo-EM data are discussed.
Article
Multidisciplinary Sciences
Baldeep Khare, Thomas Klose, Qianglin Fang, Michael G. Rossmann, Richard J. Kuhn
Summary: Usutu virus (USUV) is an emerging arbovirus in Europe that causes neuroinvasive human disease. There are currently no treatment or prevention options available due to a lack of understanding of USUV pathogenesis. Research on the mature USUV virus structure may lead to the development of therapeutics and expand knowledge on flavivirus biology.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Engineering, Biomedical
Nuphar Bianco-Stein, Iryna Polishchuk, Arad Lang, Galit Atiya, Julie Villanova, Paul Zaslansky, Alexander Katsman, Boaz Pokroy
Summary: The calcareous alga Jania sp. exhibits a highly intricate structure with helical inner pores, and each cell wall nanocrystal comprises Mg-rich calcite nanoparticles demonstrating various crystallographic orientations. This unique structure assists in preventing fracture and enhancing the alga's fracture toughness, and the presence of Mg-rich nanoparticles is also observed in another species of coralline red algae, pointing to the generality of this phenomenon.
ACTA BIOMATERIALIA
(2021)
Article
Engineering, Biomedical
Zohar Eyal, Leilah Krounbi, Oz Ben Joseph, Emanuel M. Avrahami, Iddo Pinkas, Hadas Peled-Zehavi, Assaf Gal
Summary: Biomineralization processes exhibit varying levels of control over crystallization. Coccoliths, calcified scales formed by unicellular algae, are a model for highly controlled crystallization. This study explores the relationship between base plate and coccolith properties and reveals that the combination of base plate and the chemical environment inside the cell plays a pivotal role in the exquisite control over the crystallization process.
ACTA BIOMATERIALIA
(2022)
Article
Nanoscience & Nanotechnology
Sagnik Sen, Amar Thaker, Luqmanal Sirajudeen, Dewight Williams, Brent L. Nannenga
Summary: This study demonstrates the potential of cryo-EM analysis to reveal structural details of protein-nanoparticle complexes, using GroEL-PtNP and ferritin bound to iron oxide nanoparticles as model samples.
ACS APPLIED BIO MATERIALS
(2022)
Article
Biochemistry & Molecular Biology
Yoshimasa Takizawa, Hitoshi Kurumizaka
Summary: Chromatin is a dynamic molecular complex that packages DNA in the nucleus of eukaryotic cells. Recent studies using cryo-EM have revealed the structural details of different chromatin units and their functions in the cell.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2022)
Article
Computer Science, Information Systems
Jianquan Ouyang, Yue Zhang, Kun Fang, Tianming Liu, Xiangyu Pan
Summary: This article proposes a U-Net based residual intensive neural network (Urdnet) for automatically locating particles from cryo-electron microscopy images. The experimental results show that Urdnet can achieve excellent particle picking performances comparable to mainstream methods and obtain higher resolution 3D structures of the picked particles.
CMC-COMPUTERS MATERIALS & CONTINUA
(2022)
Article
Dentistry, Oral Surgery & Medicine
H. Zhang, M. Koruyucu, F. Seymen, Y. Kasimoglu, J. -W. Kim, S. Tinawi, C. Zhang, M. L. Jacquemont, A. R. Vieira, J. P. Simmer, J. C. C. Hu
JOURNAL OF DENTAL RESEARCH
(2019)
Article
Biochemistry & Molecular Biology
Yudong Wang, Johan Palmfeldt, Niels Gregersen, Alexander M. Makhov, James F. Conway, Meicheng Wang, Stephen P. McCalley, Shrabani Basu, Hana Alharbi, Claudette St Croix, Michael J. Calderon, Simon Watkins, Jerry Vockley
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Letter
Dentistry, Oral Surgery & Medicine
Ji Won Lee, Jiwon Hong, Figen Seymen, Youn Jung Kim, Jenny Kang, Mine Koruyucu, Nuray Tuloglu, Sule Bayrak, Ji-Soo Song, Teo Jeon Shin, Hong-Keun Hyun, Young-Jae Kim, Jae-Cheoun Lee, Joo-Cheol Park, Jan Hu, James Simmer, Jung-Wook Kim
Article
Multidisciplinary Sciences
Alexis Huet, Robert L. Duda, Pascale Boulanger, James F. Conway
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Biochemistry & Molecular Biology
Nah-Young Shin, Hajime Yamazaki, Elia Beniash, Xu Yang, Seth S. Margolis, Megan K. Pugach, James P. Simmer, Henry C. Margolis
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Dentistry, Oral Surgery & Medicine
Y. J. Kim, J. Kang, F. Seymen, M. Koruyucu, H. Zhang, Y. Kasimoglu, M. Bayram, E. B. Tuna-Ince, S. Bayrak, N. Tuloglu, J. C. -C. Hu, J. P. Simmer, J. -W. Kim
JOURNAL OF DENTAL RESEARCH
(2020)
Article
Dentistry, Oral Surgery & Medicine
S. K. Wang, H. Zhang, C. Y. Hu, J. F. Liu, S. Chadha, J. W. Kim, J. P. Simmer, J. C. C. Hu
Summary: ADHCAI is a genetic disorder affecting dental enamel hardness, caused by truncation mutations in the FAM83H gene. This study characterized 9 families with ADHCAI and identified 3 novel FAM83H mutations, extending the understanding of the associated phenotypes and genotypes.
JOURNAL OF DENTAL RESEARCH
(2021)
Article
Virology
Alexis Huet, Jamie B. Huffman, James F. Conway, Fred L. Homa
JOURNAL OF VIROLOGY
(2020)
Article
Genetics & Heredity
Youn Jung Kim, Yejin Lee, Hong Zhang, Ji-Soo Song, Jan C. -C. Hu, James P. Simmer, Jung-Wook Kim
Summary: A novel de novo missense mutation in the SP6 gene was identified, causing amelogenesis imperfecta. This mutation, located at the same nucleotide positions as a previous report but with a different insertion, resulted in a much more severe clinical phenotype. The mutant protein level was significantly decreased compared to the wild-type, despite similar mRNA levels.
Article
Biochemistry & Molecular Biology
Youn Jung Kim, Yejin Lee, Hong Zhang, John Timothy Wright, James P. Simmer, Jan C. -C. Hu, Jung-Wook Kim
Summary: Amelogenesis imperfecta (AI) is a rare genetic condition affecting tooth enamel, causing insufficient enamel quantity or altered quality. A mutation in ENAM was identified in a Caucasian family with hypoplastic AI, leading to abnormal translation and reduced protein expression. This study provides insights into how a mutation in the ENAM gene can cause hypoplastic AI while maintaining normal amino acid sequence.
Article
Dentistry, Oral Surgery & Medicine
Y. J. Kim, Y. Lee, Y. Kasimoglu, F. Seymen, J. P. Simmer, J. C-C Hu, E-S Cho, J-W Kim
Summary: Amelogenesis imperfecta (AI) is a genetic disorder affecting the formation and mineralization of tooth enamel, with several genes involved including ACP4. Study of two families with hypoplastic AI revealed biallelic mutations in ACP4, resulting in decreased protein expression, homodimer formation, and acid phosphatase activity in the mutants. This expands the mutational spectrum of ACP4 and enhances understanding of its function in normal and pathological amelogenesis.
JOURNAL OF DENTAL RESEARCH
(2022)
Article
Multidisciplinary Sciences
Daniel J. Goetschius, Samantha R. Hartmann, Lindsey J. Organtini, Heather Callaway, Kai Huang, Carol M. Bator, Robert E. Ashley, Alexander M. Makhov, James F. Conway, Colin R. Parrish, Susan L. Hafenstein
Summary: The study identified a significant overlap between the antigenic epitope and the receptor binding site of canine parvovirus, showing that specific antibody binding induces conformational changes to the virus. The findings highlight the potential of using cryo-EM to investigate complementarity of antibody binding.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Herman K. H. Fung, Shelley Grimes, Alexis Huet, Robert L. Duda, Maria Chechik, Joseph Gault, Carol Robinson, Roger W. Hendrix, Paul J. Jardine, James F. Conway, Christoph G. Baumann, Alfred A. Antson
Summary: Many cellular processes rely on substrate rotation or translocation by a multi-subunit, ring-type NTPase. Researchers have reconstituted a cos packaging system and provided a detailed description of its biochemical and structural properties, revealing similarities and differences in its mechanism and regulation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Anatomy & Morphology
Charles E. Smith, Yuanyuan Hu, Mike Strauss, Jan C-C Hu, James P. Simmer
Summary: The study revealed that the distribution of focal stacks in the inner enamel of mandibular mouse incisors is not random, but rather dependent on the regional location within the transverse plane of the enamel layer. The uneven distribution of focal stacks in different regions within the inner enamel indicates a certain level of regularity and structure in their arrangement.
JOURNAL OF ANATOMY
(2021)
Review
Dentistry, Oral Surgery & Medicine
James Patrick Simmer, Nina C. Hardy, Afriti F. Chinoy, John D. Bartlett, Jan C-C. Hu
JOURNAL OF INTERNATIONAL SOCIETY OF PREVENTIVE AND COMMUNITY DENTISTRY
(2020)