Cited by 8Advanced Fluorescence Microscopy TechniquesProtein Structure and Dynamicsbioluminescence and chemiluminescence research

Allosteric modulation of fluorescence revealed by hydrogen bond dynamics in a genetically encoded maltose biosensor

Open access
Berksoz, Melike, Atilgan, Canan·2024·Proteins: Structure, Function, and Bioinformatics

Published version of a preprint

Abstract

Genetically encoded fluorescent biosensors (GEFBs) proved to be reliable tracers for many metabolites and cellular processes. In the simplest case, a fluorescent protein (FP) is genetically fused to a sensing protein which undergoes a conformational change upon ligand binding. This drives a rearrangement in the chromophore environment and changes the spectral properties of the FP. Structural determinants of successful biosensors are revealed only in hindsight when the crystal structures of both ligand‐bound and ligand‐free forms are available. This makes the development of new biosensors for desired analytes a long trial‐and‐error process. In the current study, we conducted μs‐long all atom molecular dynamics (MD) simulations of a maltose biosensor in both the apo (dark) and holo (bright) forms. We performed detailed hydrogen bond occupancy analyses to shed light on the mechanism of ligand induced conformational change in the sensor protein and its allosteric effect on the chromophore environment. We find that two strong indicators for distinguishing bright and dark states of biosensors are due to substantial changes in hydrogen bond dynamics in the system and solvent accessibility of the chromophore.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1002/prot.26688

Cites

52 of 52 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Cited by

Sorted by citations

Authors
Berksoz, M., & Atilgan, C.
Affiliations
Faculty of Engineering and Natural Sciences, Sabanci University Turkey
Venue
Proteins: Structure, Function, and Bioinformatics
Publisher
Wiley
Published
2024-04-04
Volume
92
Issue
8
Pages
923-932
ISSN
  • 0887-3585 (ISSN-L)
  • 1097-0134
OpenAlex
W4393942395
Cited by
8
References
51
Citations by year
2026: 3 · 2025: 3 · 2024: 2
FWCI
1.54
Type
journal article
Language
en
Open access
Locations
  • Proteins Structure Function and Bioinformatics (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed (publishedVersion)
  • Sabanci University (submittedVersion)
Funders
Türkiye Bilimsel ve Teknolojik Araştırma Kurumu (121Z329)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Advanced Fluorescence Microscopy Techniques
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › bioluminescence and chemiluminescence research
Keywords
genetically encoded fluorescent sensors, allosteric modulation, hydrogen bond dynamics, ligand-induced conformational change, apo and holo states, solvent accessibility, molecular dynamics simulation
MeSH terms
Allosteric Regulation, Fluorescence, Hydrogen Bonding, Ligands, Maltose, Protein Binding, Protein Conformation, Biosensing Techniques, Molecular Dynamics Simulation

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review