Biology subjects

Flatt, J. W.

Publications and source records attributed to Flatt, J. W..

4 recordsLinked to original sources

bioRxiv2025

Q-score as a reliability measure for protein, nucleic acid, and small molecule atomic coordinate models derived from 3DEM density maps

Atomic coordinate models are important in the interpretation of 3D maps produced with cryoEM and sub-tomogram averaging in cryoET, or more generically, 3D electron microscopy (3DEM). In addition to visual inspection of such maps and models, quantitative metrics convey the reliability of the atomic coordinates, in particular how well the model is supported by the experimentally determined 3DEM map. A recently introduced metric, Q-score, was shown to correlate well with the reported resolution of the map for well-fitted models. Here we present new statistical analyses of Q-scores based on its application to [~]10,000 maps and models archived in EMDB and PDB. Further we introduce two new metrics based on Q-score: Q-relative-all and Q-relative-resolution to compare a map and model to all entries in the EMDB and those with similar resolution respectively. We also explore through illustrative examples of proteins, nucleic acids, and small molecules how Q-scores can indicate whether the atomic coordinates are well-fitted to 3DEM maps and whether some parts of a map may be poorly resolved due to factors such as molecular flexibility, radiation damage, and/or conformational heterogeneity. Lastly, we show examples of how Q-scores can effectively be converted to atomic B-factors. These analyses provide a basis for how Q-scores can be interpreted effectively to evaluate 3DEM maps and atomic coordinate models prior to publication and archiving. SynopsisQ-scores are calculated each atom in models fitted to 3DEM (3D electron microscopy) maps. They measure how well the model fits the map, and also reflect the quality of the map as they correlate to resolution. Here we develop a statistical model for Q-scores applied to many maps and models in the EMDB (Electron Microscopy Database) and PDB (Protein Data Bank) respectively, and show how it can be used to assess the reliability of entire models as well as their subcomponents.

biochemistry↗

bioRxiv2020

Identification of a conserved virion-stabilizing network inside the interprotomer pocket of enteroviruses

Major efforts have been underway to develop broad-spectrum high potency capsid binders that inhibit the life cycle of enteroviruses, a large group (family Picornaviridae) whose members include poliovirus, coxsackieviruses, echoviruses, numbered enteroviruses, and rhinoviruses. These diverse viruses cause a wide variety of illnesses, ranging from the mild common cold to hand-foot-and-mouth disease, myocarditis, pancreatitis, aseptic meningitis, and encephalitis. So-called classical capsid binders target a surface exposed hydrophobic pocket in one of the viral coat proteins (VP1) to prevent the genome uncoating process. However, efficacy, toxicity, emergence of drug-resistant viruses, and existence of certain enteroviral species that lack the VP1 pocket limit their clinical benefit. Recently, we identified a new druggable site at a conserved interface formed by multiple capsid proteins, the VP1-VP3 interprotomer pocket. To further study the properties that confer druggability at this site, we have determined high-resolution cryo-electron microscopy structures of two enteroviruses, coxsackieviruses B3 and B4, complexed with interprotomer-targeting compounds, CP17 and CP48 respectively. Until now, there has been no structure available for Coxsackievirus B4 despite the fact that the virus has long been implicated in the development of insulin-dependent diabetes mellitus. At better than 3 Å resolution, we could identify the detailed interactions that facilitate ligand binding. Both compounds target the same three conserved residues, each from a different polypeptide chain, to form a virion-stabilizing network inside the pocket. We measured the in silico binding energy for both inhibitors when anchored to the network and found a global stabilizing effect on the order of thousands of kcal/mol under saturating conditions (60 total sites per virion). Intriguingly, a recent X-ray structure has revealed that glutathione targets the same network within the interprotomer site of bovine enterovirus F3, where it is thought to facilitate virus assembly. In summary, our findings provide the structural basis for how a newly designed class of capsid binders target and stabilize enteroviruses. Future efforts to chemically optimize drugs for enhanced targeting to the interprotomer pocket is a promising endeavor in the fight against enteroviruses, especially given the possibility of synergistic effects when used in combination with classical VP1 binders like pleconaril.Competing Interest StatementThe authors have declared no competing interest.View Full Text

biophysics↗

bioRxiv2019

Tracking self-citations in academic publishing

Citation metrics have value because they aim to make scientific assessment a level playing field, but urgent transparency-based adjustments are necessary to ensure that measurements yield the most accurate picture of impact and excellence. One problematic area is the handling of self-citations, which are either excluded or inappropriately accounted for when using bibliometric indicators for research evaluation. Here, in favor of openly tracking self-citations we report on self-referencing behavior among various academic disciplines as captured by the curated Clarivate Analytics Web of Science database. Specifically, we examined the behavior of 385,616 authors grouped into 15 subject areas like Biology, Chemistry, Science & Technology, Engineering, and Physics. These authors have published 3,240,973 papers that have accumulated 90,806,462 citations, roughly five percent of which are self-citations. Up until now, very little is known about the buildup of self-citations at the author-level and in field-specific contexts. Our view is that hiding self-citation data is indefensible and needlessly confuses any attempts to understand the bibliometric impact of ones work. Instead we urge academics to embrace visibility of citation data in a community of peers, which relies on nuance and openness rather than curated scorekeeping.

scientific communication and education↗

bioRxiv2018

2.8 A resolution cryo-EM structure of human parechovirus 3 in complex with Fab from a neutralizing antibody

Human parechovirus 3 (HPeV3) infection is associated with sepsis in neonates characterized by significant immune activation and subsequent tissue damage. Strategies to limit infection have been unsuccessful due to inadequate molecular diagnostic tools for early detection and lack of a vaccine or specific antiviral therapy. Towards the latter, we present a 2.8 [A]-resolution structure of HPeV3 in complex with fragments from a neutralizing human monoclonal antibody AT12-015 using cryo-EM and image reconstruction. Modeling revealed that the epitope extends across neighboring asymmetric units with contributions from capsid proteins VP0, VP1, and VP3. Antibody decoration was found to block binding of HPeV3 to cultured cells. Additionally at high-resolution, it was possible to model a stretch of RNA inside the virion and from this identify the key features that drive and stabilize protein-RNA association during assembly.\n\nImportance\n\nHPeV3 is receiving increasing attention as a prevalent cause of sepsis-like symptoms in neonates, which despite the severity of disease, there are no effective treatments available. Structural and molecular insights into virus neutralization are urgently needed, especially as clinical cases are on the rise. Towards this goal, we present the first structure of HPeV3 in complex with fragments from a neutralizing monoclonal antibody. At high-resolution it was possible to precisely define the epitope that when targeted, prevents virions from binding to cells. Such an atomic-level description is useful for understanding host-pathogen interaction, viral pathogenesis mechanisms, and for finding potential cures for infection and disease.

microbiology↗