A5007390602- Advanced Electron Microscopy Techniques and Applications
- Enzyme Structure and Function
- RNA and protein synthesis mechanisms
- Force Microscopy Techniques and Applications
- Heat shock proteins research
- DNA and Nucleic Acid Chemistry
- Electron and X-Ray Spectroscopy Techniques
- Genomics and Phylogenetic Studies
- Medical Imaging Techniques and Applications
- RNA modifications and cancer
- Protein Structure and Dynamics
- Glycosylation and Glycoproteins Research
- Hepatitis B Virus Studies
- Advanced Photocatalysis Techniques
- Endoplasmic Reticulum Stress and Disease
- Photosynthetic Processes and Mechanisms
- Advanced biosensing and bioanalysis techniques
- Bacteriophages and microbial interactions
- Quantum Dots Synthesis And Properties
- Genomics and Chromatin Dynamics
- RNA Interference and Gene Delivery
- Nanopore and Nanochannel Transport Studies
- Phytoplasmas and Hemiptera pathogens
- Advanced Nanomaterials in Catalysis
Birkbeck, University of London
2019-2025
Institute of Structural and Molecular Biology
2019-2025
Centre for Structural Systems Biology
2021-2024
Universität Hamburg
2022-2024
University Medical Center Hamburg-Eppendorf
2021-2024
Leibniz Institute of Virology (LIV)
2021-2024
University College London
2019-2021
London Centre for Nanotechnology
2019-2021
University of Leeds
2017
Abstract In the cell, DNA is arranged into highly-organised and topologically-constrained (supercoiled) structures. It remains unclear how this supercoiling affects detailed double-helical structure of DNA, largely because limitations in spatial resolution available biophysical tools. Here, we overcome these limitations, by a combination atomic force microscopy (AFM) atomistic molecular dynamics (MD) simulations, to resolve structures negatively-supercoiled minicircles at base-pair...
We present TopoStats, a Python toolkit for automated editing and analysis of Atomic Force Microscopy images. The program automates identification tracing individual molecules in circular linear conformations without user input. TopoStats was able to identify trace range within AFM images, finding, on average, ~90% all molecular assemblies wide field view, the need prior processing. DNA minicircles varying size, origami rings pore forming proteins were identified accurately traced with...
Cryo-EM experiments produce images of macromolecular assemblies that are combined to three-dimensional density maps. Typically, atomic models the constituent molecules fitted into these maps, followed by a density-guided refinement. We introduce TEMPy-ReFF, method for structure refinement in cryo-EM Our represents positions as components Gaussian mixture model, utilising their variances B-factors, which used derive an ensemble description. Extensively tested on substantial dataset 229 maps...
Abstract The Hsp70 chaperone system is capable of disassembling pathological aggregates such as amyloid fibres associated with serious degenerative diseases. Here we examine the role J-domain protein co-factor in disaggregation by Hsc70 system. We used cryo-EM and tomography to compare assemblies wild-type DNAJB1 or inactive mutants. show that binds regularly along α-synuclein fibrils acts a 2-step recruitment Hsc70, releasing auto-inhibition before activating ATPase. DNAJB1:Hsc70:Apg2...
CASP assessments primarily rely on comparing predicted coordinates with experimental reference structures. However, structures by their nature are only models themselves-their construction involves a certain degree of subjectivity in interpreting density maps and translating them to atomic coordinates. Here, we directly utilized evaluate the predictions employing method for ranking quality protein chain based fit into density. The fit-based was found correlate well assessment scores....
Abstract The power of computer simulations, including machine‐learning, has become an inseparable part scientific analysis biological data. This significantly impacted the field cryogenic electron microscopy (cryo‐EM), which grown dramatically since “resolution‐revolution.” Many maps are now solved at 3–4 Å or better resolution, although a significant proportion deposited in Electron Microscopy Data Bank still lower where positions atoms cannot be determined unambiguously. Additionally,...
Molecular structures are often fitted into cryo-EM maps by flexible fitting. When this requires large conformational changes, identifying rigid bodies can help optimize the model-map fit. Tools for in protein exist, however an equivalent nucleic acid is lacking. With increase containing RNA and progress structure prediction, there a need such tools. We previously developed RIBFIND, program clustering secondary bodies. In RIBFIND2, approach extended to structures. RIBFIND2 identify...
Abstract Coupling light‐harvesting semiconducting nanoparticles (NPs) with redox enzymes has been shown to create artificial photosynthetic systems that hold promise for the synthesis of solar fuels. High quantum yields require efficient electron transfer from nanoparticle protein, a property can be difficult control. Here, we have compared binding and between dye‐sensitized TiO 2 nanocrystals or CdS dots two decaheme cytochromes on photoanodes. The effect NP surface chemistry was assessed...
Abstract In the cell, DNA is arranged into highly-organised and topologically-constrained (supercoiled) structures. It remains unclear how this supercoiling affects detailed double-helical structure of DNA, largely because limitations in spatial resolution available biophysical tools. Here, we overcome these limitations, by a combination atomic force microscopy (AFM) atomistic molecular dynamics (MD) simulations, to resolve structures negatively-supercoiled minicircles at base-pair...
Abstract Cryo-EM experiments produce images of macromolecular assemblies that are combined to three-dimensional density maps. It is common fit atomic models the contained molecules interpret those maps, followed by a density-guided refinement. Here, we propose TEMPy-REFF, novel method for structure refinement in cryo-EM By representing positions as components mixture model, their variances B-factors, and model ensemble description, significantly improve map compared what currently achievable...
Abstract Cryo-EM experiments produce images of macromolecular assemblies that are combined to three-dimensional density maps. It is common fit atomic models the contained molecules interpret those maps, followed by a density-guided refinement. Here, we propose TEMPy-REFF, novel method for structure refinement in cryo-EM By representing positions as components mixture model, their variances B-factors, and model ensemble description, significantly improve map compared what currently achievable...
To understand the action of co-chaperones J-domain protein family in assembly disaggregation-active Hsc70 complexes on surface amyloid fibres, we used cryo-EM and tomography to compare assemblies with wild-type or an activity deficient mutant. We show that human DNAJB1 binds uniformly densely along α-synuclein fibres asymmetric orientation, one subunit dimer lying fibre other further away. It acts a 2-step recruitment first releasing auto-inhibition then activating ATPase by J domain,...
Abstract We present TopoStats, a Python toolkit for automated editing and analysis of Atomic Force Microscopy images. The program automates identification tracing individual molecules in circular linear conformations without user input. TopoStats was able to identify trace range within AFM images, finding, on average, 90% all molecular assemblies wide field view, the need prior processing. DNA minicircles varying size, origami rings pore forming proteins were identified accurately traced...
Summary Although amyloid fibres are highly stable protein aggregates, a specific combination of human Hsp70 system chaperones can disassemble them, including formed α-synuclein, huntingtin or Tau. Disaggregation requires the ATPase activity constitutively expressed Hsp70, Hsc70, together with J domain DNAJB1 and nucleotide exchange factor Apg2. Recruitment clustering Hsc70 on fibrils appear to be necessary for disassembly. Here we use atomic force microscopy (AFM) show that segments in vitro...