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Mechanical design principles of a mitotic spindle.
An organised spindle is crucial to the fidelity of chromosome segregation, but the relationship between spindle structure and function is not well understood in any cell type. The anaphase B spindle in fission yeast has a...
Cellular organization in lab-evolved and extant multicellular species obeys a maximum entropy law
Raymond Goldstein, Thomas C Day, Stephanie Hoehn, Seyed A Zamani-Dahaj, David Yanni, Anthony Burnetti, Jennifer Pentz, Aurelia R Honerkamp-Smith, Hugo Wioland, Hannah R Sleath, William C Ratcliff, Peter J Yunker
Mar 28, 2022
The prevalence of multicellular organisms is due in part to their ability to form
complex structures. How cells pack in these structures is a fundamental biophysical issue,
underlying their functional properties. However, much...
Pareto optimal metabolic engineering for the growth-coupled overproduction of sustainable chemicals.
Matteo N Amaradio, Varun Ojha, Giorgio Jansen, Massimo Gulisano, Jole Costanza, Giuseppe Nicosia
Apr 21, 2022
Our research aims to help industrial biotechnology develop a sustainable economy using green technology based on microorganisms and synthetic biology through two case studies that improve metabolic capacity in yeast models...
Cycles of autoubiquitination and deubiquitination regulate the ERAD ubiquitin ligase Hrd1.
ERAD S. cerevisiae Biochemistry Cell Biology chemical biology protein degradation protein quality control regulation Endoplasmic Reticulum Endoplasmic Reticulum-Associated Degradation Enzyme Stability Intracellular Membranes Membrane Glycoproteins Protein Domains Saccharomyces cerevisiae Saccharomyces cerevisiae Proteins Ubiquitin-Protein Ligases Ubiquitination
Cytosolic aggregation of mitochondrial proteins disrupts cellular homeostasis by stimulating the aggregation of other proteins
Urszula Nowicka, Piotr Chroscicki, Karen Stroobants, Maria Sladowska, Michal Turek, Barbara Uszczynska-Ratajczak, Rishika Kundra, Tomasz Goral, Michele Perni, Christopher M Dobson, Michele Vendruscolo, Agnieszka Chacinska
Sep 22, 2021
Screening of candidate substrates and coupling ions of transporters by thermostability shift assays.
Homa Majd, Martin S King, Shane M Palmer, Anthony C Smith, Liam Dh Elbourne, Ian T Paulsen, David Sharples, Peter Jf Henderson, Edmund RS Kunji
Nov 22, 2018
Substrates of most transport proteins have not been identified, limiting our understanding of their role in physiology and disease. Traditional identification methods use transport assays with radioactive compounds, but they are...
E. coli Microbacterium liquefaciens S. cerevisiae Tetrahymena thermophila Thermothelomyces thermophila human ion coupling molecular biophysics structural biology Substrate Specificity thermostability Adenosine Diphosphate Adenosine Triphosphate Animals Biological Assay Humans Ions Ligands Membrane Transport Proteins Mitochondria Protein Stability Reproducibility of Results Substrate Specificity Temperature Tetrahymena
Checkpoint inhibition of origin firing prevents inappropriate replication outside of S-phase
Checkpoints maintain the order of cell cycle events during DNA damage or incomplete replication. How the checkpoint response is tailored to different phases of the cell cycle remains poorly understood. The S-phase checkpoint for...
A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0.
Jasenko Zivanov, Joaquín Otón, Zunlong Ke, Andriko von Kügelgen, Euan Pyle, Kun Qu, Dustin Morado, Daniel Castaño-Díez, Giulia Zanetti, Tanmay AM Bharat, John AG Briggs, Sjors HW Scheres
Jan 05, 2023
The Role and Fate of Branch Site-U2 snRNA Interaction During Pre-mRNA Splicing
Duncan Smith
Jan 01, 0001
Many details of the conformational dynamics underlying transitions during premRNA splicing, particularly during the catalytic phase, remain unclear despite our deep knowledge of spliceosome composition. The complex assembly...
Published by: Rockefeller University
Orderly assembly underpinning built-in asymmetry in the yeast centrosome duplication cycle requires cyclin-dependent kinase
Marco Geymonat, Qiuran Peng, Zhiang Guo, Zulin Yu, Jay R Unruh, Sue L Jaspersen, Marisa Segal
Sep 04, 2020
Architecture of TAF11/TAF13/TBP complex suggests novel regulation properties of general transcription factor TFIID.
Kapil Gupta, Aleksandra A Watson, Tiago Baptista, Elisabeth Scheer, Anna L Chambers, Christine Koehler, Juan Zou, Ima Obong-Ebong, Eaazhisai Kandiah, Arturo Temblador, Adam Round, Eric Forest, Petr Man, Christoph Bieniossek, Ernest D Laue, Edward A Lemke, Juri Rappsilber, Carol V Robinson, Didier Devys, Làszlò Tora, Imre Berger
Jan 24, 2018
General transcription factor TFIID is a key component of RNA polymerase II transcription initiation. Human TFIID is a megadalton-sized complex comprising TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). TBP binds...
S. cerevisiae TBP associated factors TFIID Biochemistry biophysics core promoter DNA Gene regulation histone fold domain human structural biology Transcription Factors Crystallography X-Ray DNA Histone Acetyltransferases Humans Mass Spectrometry Promoter Regions Genetic Protein Binding Protein Conformation Protein Interaction Mapping TATA-Binding Protein Associated Factors TATA-Box Binding Protein Transcription Factor TFIID
Orderly assembly underpinning built-in asymmetry in the yeast centrosome duplication cycle requires cyclin-dependent kinase.
Marco Geymonat, Qiuran Peng, Zhiang Guo, Zulin Yu, Jay R Unruh, Sue L Jaspersen, Marisa Segal
Aug 28, 2020
Asymmetric astral microtubule organization drives the polarized orientation of the S. cerevisiae mitotic spindle and primes the invariant inheritance of the old spindle pole body (SPB, the yeast centrosome) by the bud. This...
Cellular organization in lab-evolved and extant multicellular species obeys a maximum entropy law
The prevalence of multicellular organisms is due in part to their ability to form complex structures. How cells pack in these structures is a fundamental biophysical issue, underlying their functional properties....
Thomas C Day, Stephanie S Höhn, Seyed A Zamani-Dahaj, David Yanni, Anthony Burnetti, Jennifer Pentz, Aurelia R Honerkamp-Smith, Hugo Wioland, Hannah R Sleath, William C Ratcliff, Raymond E Goldstein, Peter J Yunker
Feb 21, 2022
Folding of cohesin's coiled coil is important for Scc2/4-induced association with chromosomes.
Naomi J Petela, Andres Gonzalez Llamazares, Sarah Dixon, Bin Hu, Byung-Gil Lee, Jean Metson, Heekyo Seo, Antonio Ferrer-Harding, Menelaos Voulgaris, Thomas Gligoris, James Collier, Byung-Ha Oh, Jan Löwe, Kim A Nasmyth
Jul 28, 2021
Cohesin's association with and translocation along chromosomal DNAs depend on an ATP hydrolysis cycle driving the association and subsequent release of DNA. This involves DNA being 'clamped' by Scc2 and ATP-dependent engagement...
S. cerevisiae Chromosomes cryo-EM Folding Gene Expression molecular biophysics sister chromatid cohesion structural biology Adenosine Triphosphatases Cell Cycle Proteins Chromatids Chromosomal Proteins Non-Histone Chromosomes Cryoelectron Microscopy DNA Dimerization Gene Expression Regulation Fungal Hydrolysis Protein Domains Saccharomyces cerevisiae Saccharomyces cerevisiae Proteins
Proteotoxic Stress-induced Ribosome Stalling Does Not Significantly Impact Spontaneous Prion Formation of Sup35 or Poly-glutamine in Saccharomyces cerevisiae
Steven Janik
Jan 01, 0001
Proteins are one of the four main biological macromolecules that are central to life. Proteins are involved in a multitude of functions, such as cell signaling, intracellular regulation, and biochemical catalysis. These varying...
Published by: Ursinus College
Mechanism of completion of peptidyltransferase centre assembly in eukaryotes.
Vasileios Kargas, Pablo Castro-Hartmann, Norberto Escudero-Urquijo, Kyle Dent, Christine Hilcenko, Carolin Sailer, Gertrude Zisser, Maria J Marques-Carvalho, Simone Pellegrino, Leszek Wawiórka, Stefan MV Freund, Jane L Wagstaff, Antonina Andreeva, Alexandre Faille, Edwin Chen, Florian Stengel, Helmut Bergler, Alan John Warren
May 22, 2019
DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis.
Benjamin Jm Taylor, Serena Nik-Zainal, Yee Ling Wu, Lucy A Stebbings, Keiran Raine, Peter J Campbell, Cristina Rada, Michael R Stratton, Michael S Neuberger
Sep 29, 2018
Breast cancer genomes have revealed a novel form of mutation showers (kataegis) in which multiple same-strand substitutions at C:G pairs spaced one to several hundred nucleotides apart are clustered over kilobase-sized regions...
Global analysis of cytosine and adenine DNA modifications across the tree of life.
Sreejith Jayasree Varma, Enrica Calvani, Nana-Maria Grüning, Christoph B Messner, Nicholas Grayson, Floriana Capuano, Michael Mülleder, Markus Ralser
Jul 28, 2022
Interpreting the function and metabolism of enzymatic DNA modifications requires both position-specific and global quantities. Sequencing-based techniques that deliver the former have become broadly accessible, but analytical...
RNA promotes phase separation of glycolysis enzymes into yeast G bodies in hypoxia.
Gregory G Fuller, Ting Han, Mallory A Freeberg, James J Moresco, Amirhossein Ghanbari Niaki, Nathan P Roach, John R Yates, Sua Myong, John K Kim
Apr 17, 2020
In hypoxic stress conditions, glycolysis enzymes assemble into singular cytoplasmic granules called glycolytic (G) bodies. G body formation in yeast correlates with increased glucose consumption and cell survival. However, the...
Global analysis of cytosine and adenine DNA modifications across the tree of life.
Sreejith Jayasree Varma, Enrica Calvani, Nana-Maria Grüning, Christoph B Messner, Nicholas Grayson, Floriana Capuano, Michael Mülleder, Markus Ralser
Sep 02, 2022
Transport of DNA within cohesin involves clamping on top of engaged heads by Scc2 and entrapment within the ring by Scc3.
James E Collier, Byung-Gil Lee, Maurici Brunet Roig, Stanislav Yatskevich, Naomi J Petela, Jean Metson, Menelaos Voulgaris, Andres Gonzalez Llamazares, Jan Löwe, Kim A Nasmyth
Sep 16, 2020
In addition to extruding DNA loops, cohesin entraps within its SMC-kleisin ring (S-K) individual DNAs during G1 and sister DNAs during S-phase. All three activities require related hook-shaped proteins called Scc2 and Scc3....
Visualizing the functional architecture of the endocytic machinery.
Clathrin-mediated endocytosis is an essential process that forms vesicles from the plasma membrane. Although most of the protein components of the endocytic protein machinery have been thoroughly characterized, their...
A protein quality control pathway at the mitochondrial outer membrane.
Meredith B Metzger, Jessica L Scales, Mitchell F Dunklebarger, Jadranka Loncarek, Allan M Weissman
Apr 06, 2020
Maintaining the essential functions of mitochondria requires mechanisms to recognize and remove misfolded proteins. However, quality control (QC) pathways for misfolded mitochondrial proteins remain poorly defined. Here, we...
MAD S. cerevisiae UPS Cell Biology misfolded Quality Control Yeast Cytosol Intracellular Membranes Mitochondrial Proteins Molecular Chaperones Proteasome Endopeptidase Complex Protein Binding Protein Transport Proteolysis Saccharomyces cerevisiae Saccharomyces cerevisiae Proteins Temperature Ubiquitin Ubiquitin-Protein Ligases
Cytosolic aggregation of mitochondrial proteins disrupts cellular homeostasis by stimulating the aggregation of other proteins.
Urszula Nowicka, Piotr Chroscicki, Karen Stroobants, Maria Sladowska, Michal Turek, Barbara Uszczynska-Ratajczak, Rishika Kundra, Tomasz Goral, Michele Perni, Christopher M Dobson, Michele Vendruscolo, Agnieszka Chacinska
Oct 18, 2021
Mitochondria are organelles with their own genomes, but they rely on the import of nuclear-encoded proteins that are translated by cytosolic ribosomes. Therefore, it is important to understand whether failures in the...
C. elegans S. cerevisiae AGGREGATION Biochemistry chaperones chemical biology Homeostasis metastable proteins Mitochondria neurodegeneration Alzheimer Disease Animals Caenorhabditis elegans Caenorhabditis elegans Proteins Cytosol Databases Genetic HEAT-SHOCK PROTEINS Humans Mitochondria Mitochondrial Proteins Molecular Chaperones Protein Aggregates Protein Transport Proteostasis Saccharomyces cerevisiae Saccharomyces cerevisiae Proteins