Computational design of a genetically encoded iron biosensor

Download

HIBIT_Paper_Melike_Berksöz_acknow.pdf

Date

2022-10

Author

Berksöz, Melike
Atılgan, Canan

Metadata

Show full item record

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Item Usage Stats

535
views

116
downloads

Genetically encoded fluorescent biosensors (GEFB) 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 determined 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 this work, we propose a novel design strategy that combines Alphafold2 (AF2) and all-atom molecular dynamics (MD) simulations as predictors of GEFB structure and dynamics. H. influenza ferric binding protein (FBP) is selected as a model sensor protein. Hydrogen bond occupancies around the chromophore are analyzed in apo and holo states of fused FBP. Hydrogen bond profile of intact GFP alone with neutral and anionic chromophore was used as a reference for dark and bright states respectively.

URI

https://hibit2022.ims.metu.edu.tr/
https://hdl.handle.net/11511/101300

Conference Name

The International Symposium on Health Informatics and Bioinformatics

Collections

Graduate School of Informatics, Conference / Seminar

Suggestions

OpenMETU
Core

Integration of a Genetically Encoded Calcium Molecular Sensor into Photopolymerizable Hydrogels for Micro-Optrode-Based Sensing Kahyaoğlu, Leyla Nesrin; Park, Joon Hyeong; Rickus, Jenna L. (American Chemical Society (ACS), 2017-09-20) Genetically encoded molecular-protein sensors (GEMS) are engineered to sense and quantify a wide range of biological substances and events in cells, in vitro and even in vivo with high spatial and temporal resolution. Here, we aim to stably incorporate these proteins into a photopatternable matrix, while preserving their functionality, to extend the application of these proteins as spatially addressable optical biosensors. For this reason, we examined the fabrication of 3D hydrogel microtips doped with a ge...
STATISTICAL MODELING OF THE GEOMETRIC ERROR IN CARDIAC ELECTRICAL IMAGING Aydin, Umit; Serinağaoğlu Doğrusöz, Yeşim (2009-07-01) Kalman filter approach provides a natural way to include the spatio-temporal prior information in cardiac electrical imaging. This study focuses on the performance of Kalman filter approach with geometric errors present in inverse Electrocardiography (ECG) problem. The geometric errors considered here are the wrong determination of the heart's size and location. In addition to Kalman filtering, we also compare the performances of Tikhonov regularization and Bayesian MAP estimation when geometric errors are ...
Assessment of effects of multi drug resistance on dielectric properties of K562 leukemic cells using electrorotation Bahrieh, Garsha; Erdem, Murat; Ozgur, Ebru; Gündüz, Ufuk; Külah, Haluk (2014-01-01) In this study, dielectric characterization of multidrug resistant (MDR) K562 human leukemia cells was carried out using a MEMS based electrorotation (ER) device with 3D electrodes. P-glycoprotein (P-gp) dependent MDR causes variation in cell dielectric properties (cell interior conductivity (sigma(i)), membrane capacitance (C-m) and total effective membrane conductance (G(m)*)) due to overexpression of P-gp, which modulates the activity of membrane-bound Cl- channels. Different cell populations resistant to...
Computational studies of cyclobutadiene and benzocyclobutene fused to p- and o-quinone McKee, ML; Balcı, Metin; Kilic, H; Yurtsever, E (1998-03-26) Cyclobutadiene and benzocyclobutenes fused to o- and p-quinone have been studied by computational methods. Geometries were optimized at the B3LYP/6-31G* level, and absolute NMR shielding values were calculated using the GIAO method with the HF/6-31G* basis set. NICS values of the compounds 8b,c and 9b,c indicate strong antiaromatic character for cyclobutadiene units. However, 8a and 9a show negative NICS values where the quinodal system reduces the antiaromaticity significantly by forcing these systems to p...
Computational modelling of electro-active polymers Dal, Sinan Fırat; Göktepe, Serdar; Department of Civil Engineering (2019) This study is concerned with the stability of Electro-Active Polymers (EAPs) having geometries with periodic microstructures subjected to coupled electromechanical effects. For this purpose, coupled electromechanical equations, which are nonlinear, are discretized using the Finite Element Method (FEM) under the prescribed boundary conditions. EAPs are smart materials that may undergo large mechanical deformations when subjected to an electric field. Unlike many other materials that show permanent deformatio...

Citation Formats

M. Berksöz and C. Atılgan, “Computational design of a genetically encoded iron biosensor,” Erdemli, Mersin, TÜRKİYE, 2022, p. 1030, Accessed: 00, 2023. [Online]. Available: https://hibit2022.ims.metu.edu.tr/.