Pranav N. M. Shah
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View article: Remodelled cholesteryl ester enriched lipid droplets fuel flavivirus morphogenesis
Remodelled cholesteryl ester enriched lipid droplets fuel flavivirus morphogenesis Open
Flaviviruses such as dengue and Zika viruses extensively remodel host cell membranes to create specialised replication organelles, but the role of lipid metabolism to generate them remain poorly understood. Through systematic screens of fa…
View article: Incorporating a Deep Neural Network into Moving Horizon Estimation for Embedded Thermal Torque Derating of an Electric Machine
Incorporating a Deep Neural Network into Moving Horizon Estimation for Embedded Thermal Torque Derating of an Electric Machine Open
This study introduces a novel state estimation framework that incorporates Deep Neural Networks (DNNs) into Moving Horizon Estimation (MHE), shifting from traditional physics-based models to rapidly developed data-driven techniques. A DNN …
View article: <i>TomoCPT</i>: a generalizable model for 3D particle detection and localization in cryo-electron tomograms
<i>TomoCPT</i>: a generalizable model for 3D particle detection and localization in cryo-electron tomograms Open
Cryo-electron tomography is a rapidly developing field for studying macromolecular complexes in their native environments and has the potential to revolutionize our understanding of protein function. However, fast and accurate identificati…
View article: Validation data for macromolecular occupancy estimation
Validation data for macromolecular occupancy estimation Open
Macromolecular densities used to validate OccuPy v0.1: Synthetic densities of pdb 1UXI with altered: Occupancy of chain A Occupancy of NAD cofactors Bfactor of chain A at occupancy 0.5 of chain A Reconstructions of rotavirus spike protein:…
View article: Validation data for macromolecular occupancy estimation
Validation data for macromolecular occupancy estimation Open
Macromolecular densities used to validate OccuPy v0.1: Synthetic densities of pdb 1UXI with altered: Occupancy of chain A Occupancy of NAD cofactors Bfactor of chain A at occupancy 0.5 of chain A Reconstructions of rotavirus spike protein:…
View article: A robust normalized local filter to estimate compositional heterogeneity directly from cryo-EM maps
A robust normalized local filter to estimate compositional heterogeneity directly from cryo-EM maps Open
Cryo electron microscopy (cryo-EM) is used by biological research to visualize biomolecular complexes in 3D, but the heterogeneity of cryo-EM reconstructions is not easily estimated. Current processing paradigms nevertheless exert great ef…
View article: Delineating organizational principles of the endogenous L-A virus by cryo-EM and computational analysis of native cell extracts
Delineating organizational principles of the endogenous L-A virus by cryo-EM and computational analysis of native cell extracts Open
The high abundance of most viruses in infected host cells benefits their structural characterization; endogenous viruses are present in low copy numbers, however, and are therefore challenging to investigate. Here, we retrieve cell extract…
View article: Cryo-EM structures reveal two distinct conformational states in a picornavirus cell entry intermediate
Cryo-EM structures reveal two distinct conformational states in a picornavirus cell entry intermediate Open
The virions of enteroviruses such as poliovirus undergo a global conformational change after binding to the cellular receptor, characterized by a 4% expansion, and by the opening of holes at the two and quasi-three-fold symmetry axes of th…
View article: The SARS-CoV-2 Spike harbours a lipid binding pocket which modulates stability of the prefusion trimer
The SARS-CoV-2 Spike harbours a lipid binding pocket which modulates stability of the prefusion trimer Open
Summary Large trimeric Spikes decorate SARS-CoV-2 and bind host cells via receptor binding domains (RBDs). We report a conformation in which the trimer is ‘locked’ into a compact well-ordered form. This differs from previous structures whe…
View article: Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient
Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient Open
The COVID-19 pandemic has had unprecedented health and economic impact, but currently there are no approved therapies. We have isolated an antibody, EY6A, from a late-stage COVID-19 patient and show it neutralises SARS-CoV-2 and cross-reac…
View article: Structural characterisation of a nanobody derived from a naïve library that neutralises SARS-CoV-2
Structural characterisation of a nanobody derived from a naïve library that neutralises SARS-CoV-2 Open
The SARS-CoV-2 virus is more transmissible than previous coronaviruses and causes a more serious illness than seasonal flu. The SARS-CoV-2 receptor binding domain (RBD) of the Spike protein binds to the human angiotensin-converting enzyme …
View article: Neutralization of SARS-CoV-2 by destruction of the prefusion Spike
Neutralization of SARS-CoV-2 by destruction of the prefusion Spike Open
Summary There are as yet no licenced therapeutics for the COVID-19 pandemic. The causal coronavirus (SARS-CoV-2) binds host cells via a trimeric Spike whose receptor binding domain (RBD) recognizes angiotensin-converting enzyme 2 (ACE2), i…
View article: Cryo-EM structures reveal two distinct conformational states in a picornavirus cell entry intermediate
Cryo-EM structures reveal two distinct conformational states in a picornavirus cell entry intermediate Open
The virions of enteroviruses such as poliovirus undergo a global conformational change after binding to the cellular receptor, characterized by a 4% expansion, and opening of holes at the two and quasi-three-fold symmetry axes of the capsi…
View article: Surface Immobilization of Viruses and Nanoparticles Elucidates Early Events in Clathrin-Mediated Endocytosis
Surface Immobilization of Viruses and Nanoparticles Elucidates Early Events in Clathrin-Mediated Endocytosis Open
Clathrin-mediated endocytosis (CME) is an important entry pathway for viruses. Here, we applied click chemistry to covalently immobilize reovirus on surfaces to study CME during early host-pathogen interactions. To uncouple chemical and ph…
View article: Genome packaging of reovirus is mediated by the scaffolding property of the microtubule network
Genome packaging of reovirus is mediated by the scaffolding property of the microtubule network Open
Reovirus replication occurs in the cytoplasm of the host cell, in virally induced mini-organelles called virus factories. On the basis of the serotype of the virus, the virus factories can manifest as filamentous (type 1 Lang strain) or gl…