Evidence map›Paper›PMID 42663956›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2026

Simulation of pH-Dependent, Loop-Based Membrane Protein Gating Using Pretzel.

Alan Perez-Rathke, Monifa A V Fahie, Christina M Chisholm, Min Chen, Jie Liang

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Article in Methods in molecular biology (Clifton, N.J.), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed
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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

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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

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Alan Perez-RathkeDepartment of Bioengineering, University of Illinois at Chicago, Chicago, IL, 60607, USA.
Monifa A V FahieMolecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA, 01003, USA.
Christina M ChisholmMolecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA, 01003, USA.
Min ChenMolecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA, 01003, USA.
Jie LiangDepartment of Bioengineering, University of Illinois at Chicago, Chicago, IL, 60607, USA. jliang@uic.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Bacterial porins often exhibit ion conductance and gating behavior, which can be modulated by pH. However, the underlying control mechanism of gating is often complex, and direct inspection of the protein structure is generally insufficient for full mechanistic understanding. Here we describe Pretzel, a computational framework that can effectively model loop-based gating events in membrane proteins. Our method combines Monte Carlo conformational sampling, structure clustering, ensemble energy evaluation, and a topological gating criterion to model the equilibrium gating state under the pH environment of interest. We discuss details of applying Pretzel to the porin Outer membrane protein G (OmpG).

Indexed as

Bacterial Outer Membrane ProteinsIon Channel GatingPorinsComputer SimulationEscherichia coli ProteinsHydrogen-Ion ConcentrationModels, MolecularMonte Carlo MethodProtein ConformationBacterial Outer Membrane ProteinsEscherichia coli ProteinsOmpG protein, E coliPorinsBacterial outer membrane proteinsClusteringComputer simulationIon channel gatingOmpG proteinProtein conformationProtein loop modelingSequential Monte Carlo sampling

Identifiers

PMID42663956

What OpenQuestion holds

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Registered trials

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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 OpenQuestion graph.