Loop region mutations in Omp33-36: unveiling reduced antimicrobial permeability and resistance in Acinetobacter baumannii through structural modeling and membrane-protein simulations
6 affiliations
- 1Division of Bacteriology, ICMR National Institute for Research in Bacterial Infections (ICMR-NIRBI)
- 2Department of Bioscience and Bioengineering, Indian Institute of Technology Roorkee (IITR)
- 3Department of Physics, Indian Institute of Technology Roorkee (IITR)
- 4Department of Botany and Microbiology, Gurukula Kangri (Deemed to Be University)
- 5Centre of Excellence for Chemical Mechanisms of Life, Uppsala University
- 6Centre for Nanotechnology, Indian Institute of Technology Roorkee (IITR)
Abstract
Background: Acinetobacter baumannii can reduce its susceptibility to antimicrobials by altering the permeability of the outer membrane, e.g., by changing the abundance and function of porins. Omp33-36 has been implicated in susceptibility to multiple antibiotics including carbapenems, but the structural effect of sequence variations observed in clinical isolates is poorly understood. We investigated whether substitutions in Omp33-36 from multidrug-resistant clinical isolates affect porin dynamics and contribute to permeability-related resistance.
Methods: Multilocus sequence typing identified lineages and Sanger sequencing identified Omp33-36 substitutions in A. baumannii bloodstream isolates. The expression of omp33-36 was measured by reverse transcription quantitative polymerase chain reaction (RT-qPCR) and the acquired resistance determinants were analyzed by PCR. Based on the experimentally determined structure (PDB 6GIE), we built full-length wild-type and variant models of Omp33-36, embedded them into a phospholipid bilayer and performed all-atom molecular dynamics simulations to study their conformational behavior, residue mobility and loop-associated interactions.
Results: Two multidrug-resistant isolates with reduced omp33-36 expression harbored substitutions Phe125Asn/Glu243Ser (A_146) and Gly248Asp/Asp250Asn (A_106). The β-barrel scaffold was stable, but substitutions affected local packing, interaction network and loop dynamics. Phe125Asn reduced steric constraints and allowed more polar interactions. Mutations in the Gly242-Gly252 region created new local and cross-region contacts that constrained conformational freedom. These changes favored conformational states with increased mechanical constraints and without global destabilization. The observations are consistent with a working two-gate coupled motion model in which extracellular- and periplasmic-facing access regions are dynamically coupled components. The mutation-associated change in loop dynamics and preference for less-accessible channel states may disrupt coordination, but no direct evidence for diminished antibiotic flux was provided.
Conclusion: Substitutions in Omp33-36 alter local networks of interactions and loop dynamics but preserve the β-barrel architecture. These changes and a reduced expression of porins may result in changes in permeability. However, the presence of other resistance determinants makes Omp33-36 changes a possible contributor to a multifactorial resistance phenotype rather than an independently demonstrated cause. Direct measurements of permeability and isogenic studies with expression control are necessary to validate the proposed mechanism.
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BibTeX
@article{roy2026loop,
title = {{Loop region mutations in Omp33-36: unveiling reduced antimicrobial permeability and resistance in Acinetobacter baumannii through structural modeling and membrane-protein simulations}},
author = {Subhasree Roy and Khalid Ansari and Mousumi Hazra and Vivek Junghare and Tanusree Das and Arup Samanta and Sulagna Basu and Saugata Hazra},
journal = {Frontiers in Microbiology},
year = {2026},
month = oct,
doi = {10.3389/fmicb.2026.1954565},
url = {https://www.frontiersin.org/articles/10.3389/fmicb.2026.1954565/full},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Loop region mutations in Omp33-36: unveiling reduced antimicrobial permeability and resistance in Acinetobacter baumannii through structural modeling and membrane-protein simulations
AU - Subhasree Roy
AU - Khalid Ansari
AU - Mousumi Hazra
AU - Vivek Junghare
AU - Tanusree Das
AU - Arup Samanta
AU - Sulagna Basu
AU - Saugata Hazra
PY - 2026
DA - 2026/10/20
JO - Frontiers in Microbiology
DO - 10.3389/fmicb.2026.1954565
UR - https://www.frontiersin.org/articles/10.3389/fmicb.2026.1954565/full
AB - Background: Acinetobacter baumannii can reduce its susceptibility to antimicrobials by altering the permeability of the outer membrane, e.g., by changing the abundance and function of porins. Omp33-36 has been implicated in susceptibility to multiple antibiotics including carbapenems, but the structural effect of sequence variations observed in clinical isolates is poorly understood. We investigated whether substitutions in Omp33-36 from multidrug-resistant clinical isolates affect porin dynamics and contribute to permeability-related resistance. Methods: Multilocus sequence typing identified lineages and Sanger sequencing identified Omp33-36 substitutions in A. baumannii bloodstream isolates. The expression of omp33-36 was measured by reverse transcription quantitative polymerase chain reaction (RT-qPCR) and the acquired resistance determinants were analyzed by PCR. Based on the experimentally determined structure (PDB 6GIE), we built full-length wild-type and variant models of Omp33-36, embedded them into a phospholipid bilayer and performed all-atom molecular dynamics simulations to study their conformational behavior, residue mobility and loop-associated interactions. Results: Two multidrug-resistant isolates with reduced omp33-36 expression harbored substitutions Phe125Asn/Glu243Ser (A_146) and Gly248Asp/Asp250Asn (A_106). The β-barrel scaffold was stable, but substitutions affected local packing, interaction network and loop dynamics. Phe125Asn reduced steric constraints and allowed more polar interactions. Mutations in the Gly242-Gly252 region created new local and cross-region contacts that constrained conformational freedom. These changes favored conformational states with increased mechanical constraints and without global destabilization. The observations are consistent with a working two-gate coupled motion model in which extracellular- and periplasmic-facing access regions are dynamically coupled components. The mutation-associated change in loop dynamics and preference for less-accessible channel states may disrupt coordination, but no direct evidence for diminished antibiotic flux was provided. Conclusion: Substitutions in Omp33-36 alter local networks of interactions and loop dynamics but preserve the β-barrel architecture. These changes and a reduced expression of porins may result in changes in permeability. However, the presence of other resistance determinants makes Omp33-36 changes a possible contributor to a multifactorial resistance phenotype rather than an independently demonstrated cause. Direct measurements of permeability and isogenic studies with expression control are necessary to validate the proposed mechanism.
SN - 1664-302X
ER -