Evidence map›Paper›PMID 41125214›Full record

ArticleJournal of structural biology2025

Local microenvironments of capsomer variants in the PBCV-1.

Wenhan Guo, Esther Alarcon, Jason E Sanchez, Chuan Xiao, Lin Li

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of structural biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

5 authors.

Wenhan GuoDepartment of Physics, University of Texas at El Paso, El Paso, TX, USA; Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, TX, USA.
Esther AlarconDepartment of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, TX, USA.
Jason E SanchezDepartment of Computational Science, University of Texas at El Paso, El Paso, TX, USA.
Chuan XiaoDepartment of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, TX, USA; Department of Computational Science, University of Texas at El Paso, El Paso, TX, USA; Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX, USA. Electronic address: cxiao@utep.edu.
Lin LiDepartment of Physics, University of Texas at El Paso, El Paso, TX, USA; Department of Computational Science, University of Texas at El Paso, El Paso, TX, USA; Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX, USA. Electronic address: lli5@utep.edu.

Funding

UTEP Border Biomedical Research CenterU54MD007592 · NIMHD · UNIVERSITY OF TEXAS EL PASO · PI Robert A. Kirken · 2019 to 2026
$35.1M
Deciphering the Molecular Assembly Mechanism of Giant DNA VirusesR01GM129525 · NIGMS · UNIVERSITY OF TEXAS EL PASO · PI XIAO, CHUAN · 2019 to 2023
$1.8M
Developing and applying large-scale simulation approach to understand the mechanisms of kinesins' motilities along microtubulesSC1GM132043 · NIGMS · UNIVERSITY OF TEXAS EL PASO · PI LI, LIN · 2019 to 2022
$1.5M
NIGMS NIH HHS R01 GM129525NIGMS NIH HHS SC1 GM132043NIMHD NIH HHS U54 MD007592
6 · The paper itself

Abstract

PBCV-1, a giant virus classified among the Nucleocytoviricota virus (NCV) whose structure has been determined to near atomic resolution. The majority capsomers forming the capsid of PBCV-1 are Type I capsomers while five other type of variants have been found in recent high resolution structure. Interestingly, some variants, such as Type V capsomers, are found at particular capsid locations whose roles are unclear. To reveal the roles of a Type V capsomer, we replaced the Type V capsomer by a Type I capsomer to compare the interaction among the two types of capsomer variant, especially the interactions between each of the Type V/Type I capsomer and its local capsid microenvironment. Our results revealed significant differences between Type V and Type I capsomers. Notably, the Type V capsomer demonstrated a stronger binding force to the surrounding capsomers than the Type I capsomer. Moreover, the identified salt bridges between Type V/I capsomers and their surrounding capsomers corroborate the results of electrostatic calculations, further highlighting the important residues involved in these interactions. Understanding these local capsid microenvironments will be essential to elucidate the mechanisms governing viral capsid assembly.

Indexed as

CapsidCapsid ProteinsModels, MolecularCapsid ProteinsCapsid assemblyElectrostatic featuresMajor Capsid ProteinMolecular Dynamics simulationPBCB-1

Identifiers

PMID41125214
PMCPMC13204982

What Socratic holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.