A5087861735- RNA and protein synthesis mechanisms
- Advanced Electron Microscopy Techniques and Applications
- Bacteriophages and microbial interactions
- RNA modifications and cancer
- RNA Research and Splicing
- Electron and X-Ray Spectroscopy Techniques
- Bacterial Genetics and Biotechnology
- Nuclear Structure and Function
- Genomics and Phylogenetic Studies
- Photosynthetic Processes and Mechanisms
- Enzyme Catalysis and Immobilization
- Enzyme Structure and Function
- Protein Structure and Dynamics
- Parkinson's Disease Mechanisms and Treatments
- Microbial Metabolic Engineering and Bioproduction
- Microtubule and mitosis dynamics
- Genomics and Chromatin Dynamics
- Angiogenesis and VEGF in Cancer
- DNA and Nucleic Acid Chemistry
- Peptidase Inhibition and Analysis
- Cellular Mechanics and Interactions
- Ion-surface interactions and analysis
- Electrochemical sensors and biosensors
- Crystallization and Solubility Studies
- Monoclonal and Polyclonal Antibodies Research
University of California, San Diego
2016-2025
Howard Hughes Medical Institute
2021-2025
UC San Diego Health System
2024-2025
Research Network (United States)
2024
University of Illinois Urbana-Champaign
2004-2018
Max Planck Institute of Biochemistry
2009-2016
Max Planck Society
2009-2013
Ludwig-Maximilians-Universität München
2012
Center for Integrated Protein Science Munich
2012
TU Dortmund University
2003-2010
Abstract NAMD is a parallel molecular dynamics code designed for high‐performance simulation of large biomolecular systems. scales to hundreds processors on high‐end platforms, as well tens low‐cost commodity clusters, and also runs individual desktop laptop computers. works with AMBER CHARMM potential functions, parameters, file formats. This article, directed novices experts, first introduces concepts methods used in the program, describing classical force field, equations motion,...
Close-up view of the nuclear periphery Cell biologists would like to be able visualize complexes inside cells at molecular resolution. Several limitations, however, have prevented field from realizing this goal. The thickness most precludes cryo-electron tomography, a technique which itself does not provide sufficient contrast. Mahamid et al. successfully combined recent advances on both fronts analyze structures in situ nucleus. Their images reveal features that inform our understanding...
The 26S proteasome is at the executive end of ubiquitin-proteasome pathway for controlled degradation intracellular proteins. While structure its 20S core particle (CP) has been determined by X-ray crystallography, 19S regulatory (RP), which recruits substrates, unfolds them, and translocates them to CP degradation, remained elusive. Here, we describe molecular architecture holocomplex an integrative approach based on data from cryoelectron microscopy, residue-specific chemical...
Cryoelectron tomography provides unprecedented insights into the macromolecular and supramolecular organization of cells in a close-to-living state. However because limited thickness range (< 0.5–1 μm) that is accessible with today’s intermediate voltage electron microscopes only small prokaryotic or peripheral regions eukaryotic can be examined directly. Key to overcoming this limitation ability prepare sufficiently thin samples. Cryosectioning used enough sections but suffers from...
Abstract The multifunctional nucleocapsid (N) protein in SARS-CoV-2 binds the ~30 kb viral RNA genome to aid its packaging into 80–90 nm membrane-enveloped virion. N is composed of N-terminal RNA-binding and C-terminal dimerization domains that are flanked by three intrinsically disordered regions. Here we demonstrate protein’s central domain drives phase separation with RNA, phosphorylation an adjacent serine/arginine rich region modulates physical properties resulting condensates. In...
Chloroplast function is orchestrated by the organelle's intricate architecture. By combining cryo-focused ion beam milling of vitreous Chlamydomonas cells with cryo-electron tomography, we acquired three-dimensional structures chloroplast in its native state within cell. envelope inner membrane invaginations were frequently found close association thylakoid tips, and tips multiple stacks converged at dynamic sites on envelope, implicating lipid transport biogenesis. Subtomogram averaging...
The RNA binding protein TDP-43 forms intranuclear or cytoplasmic aggregates in age-related neurodegenerative diseases. In this study, we found that binding-deficient (produced by neurodegeneration-causing mutations posttranslational acetylation its recognition motifs) drove demixing into liquid spherical shells with cores. These droplets, which named "anisosomes", have exhibit birefringence, thus indicating crystal formation. Guided mathematical modeling, identified the primary components of...
Expression of the Escherichia coli tryptophanase operon depends on ribosome stalling during translation upstream TnaC leader peptide, a process for which interactions between nascent chain and ribosomal exit tunnel are critical. We determined 5.8 angstrom-resolution cryo-electron microscopy single-particle reconstruction stalled tnaC gene. The was extended within tunnel, making contacts with components at distinct sites. Upon stalling, two conserved residues peptidyltransferase center...
The 26S proteasome operates at the executive end of ubiquitin-proteasome pathway. Here, we present a cryo-EM structure Saccharomyces cerevisiae resolution 7.4 Å or 6.7 (Fourier-Shell Correlation 0.5 0.3, respectively). We used this map in conjunction with molecular dynamics-based flexible fitting to build near-atomic model holocomplex. quality allowed us assign α-helices, predominant secondary element regulatory particle subunits, throughout entire map. were able determine architecture...
We observed the assembly of a nucleus-like structure in bacteria during viral infection. Using fluorescence microscopy and cryo-electron tomography, we showed that Pseudomonas chlororaphis phage 201φ2-1 assembled compartment separated DNA from cytoplasm. The was centered by bipolar tubulin-based spindle, it segregated bacterial proteins according to function. Proteins involved replication transcription localized inside compartment, whereas translation nucleotide synthesis outside. Later...
Nuclear pore complexes (NPCs) mediate the nucleocytoplasmic transport of macromolecules. Here we provide a structure isolated yeast NPC in which inner ring is resolved by cryo-EM at sub-nanometer resolution to show how flexible connectors tie together different structural and functional layers. These may be targets for phosphorylation regulated disassembly cells with an open mitosis. Moreover, some nucleoporin pairs factors have similar interaction motifs, suggests evolutionary mechanistic...
Intracellular phase separation is emerging as a universal principle for organizing biochemical reactions in time and space. It remains incompletely resolved how biological function encoded these assemblies whether this depends on their material state. The conserved intrinsically disordered protein PopZ forms condensates at the poles of bacterium Caulobacter crescentus, which turn orchestrate cell-cycle regulating signaling cascades. Here we show that properties are determined by balance...
Abstract Bacteria encode myriad defences that target the genomes of infecting bacteriophage, including restriction–modification and CRISPR–Cas systems 1 . In response, one family large bacteriophages uses a nucleus-like compartment to protect its replicating by excluding host defence factors 2–4 However, principal composition structure this remain unknown. Here we find bacteriophage nuclear shell assembles primarily from protein, which name chimallin (ChmA). Combining cryo-electron...
The nuclear pore complex (NPC) is the sole mediator of nucleocytoplasmic transport. Despite great advances in understanding its conserved core architecture, peripheral regions can exhibit considerable variation within and between species. One such structure cage-like basket. crucial roles mRNA surveillance chromatin organization, an architectural has remained elusive. Using in-cell cryo-electron tomography subtomogram analysis, we explored NPC's structural variations basket across fungi...
In translation, elongation factor Tu (EF-Tu) molecules deliver aminoacyl-tRNAs to the mRNA-programmed ribosome. The GTPase activity of EF-Tu is triggered by ribosome-induced conformational changes that play a pivotal role in selection cognate aminoacyl-tRNAs. We present 6.7-Å cryo-electron microscopy map aminoacyl-tRNA·EF-Tu·GDP·kirromycin-bound Escherichia coli ribosome, together with an atomic model complex obtained through molecular dynamics flexible fitting. reveals conserved switch...
Protein biosynthesis, the translation of genetic code into polypeptides, occurs on ribonucleoprotein particles called ribosomes. Although X-ray structures bacterial ribosomes are available, high-resolution eukaryotic 80S lacking. Using cryoelectron microscopy and single-particle reconstruction, we have determined structure a translating plant ( Triticum aestivum ) ribosome at 5.5-Å resolution. This map, together with 6.1-Å map Saccharomyces cerevisiae ribosome, has enabled us to model ∼98%...