Decoding the effect of temperatures on conformational stability and order of ligand unbound thermosensing adenine riboswitch using molecular dynamics simulation
Creators: name: Das, Soumi
Publisher: name: Taylor & Francis
Year: 2025
Subjects: Biophysics
Biochemistry
Physical Sciences not elsewhere classified
Molecular Biology
Biotechnology
Chemical Sciences not elsewhere classified
Astronomical and Space Sciences not elsewhere classified
Hematology
Computational Biology

description: The structure-function relationship of the riboswitch is governed mainly by two factors, ligand binding and temperature. Most of the experimental studies shed light on structural dynamics and gene regulation function of Adenine riboswitch from the aspect of ligand instead of temperature. Two unliganded Adenine riboswitch conformations (apoA and apoB) from the thermophile <i>Vibrio vulnificus</i> draw particular attention due to their diverse and polymorphic structures. Ligand-free apoB Adenine riboswitch conformation is not able to interact with the ligand whereas ligand-free apoA Adenine riboswitch conformation adopts ligand-receptive form. The interconversion between apoA and apoB conformation is temperature-dependent and thermodynamically controlled. Therefore Adenine riboswitch is called temperature sensing RNA. The molecular mechanism underlying the thermosensitivity of ligand free Adenine riboswitch is not well known. Hence an attempt is made to examine conformational stability and order of apoA with respect to apoB Adenine riboswitch aptamer computing RMSD, RMSF, R<sub>G</sub>, principal component analysis, hydrogen bonding interaction and conformational thermodynamics derived from all-atom molecular dynamics trajectories in the temperature range 283K-400K. The temperatures corresponding to the conformational stability and order of apoA adenine riboswitch with respect to apoB adenine riboswitch whole aptamer are shown in descending order 293K∼303K&gt; 313K∼283K&gt;373K&gt;323K. Residue wise and domain wise changes in conformational free energy and entropy of conformational degrees of freedom like pseudo-torsion angle ƞ and θ reflect apoA exhibits pronounced conformational stability compared to apoB at temperatures 293K and 303K, whereas both forms reveal decreased stability at 323K and 400K and may be inactivated, highlighting their role as temperature sensors. Molecular Dynamics Simulation of ligand unbound two different conformations of adenine riboswitch with the same sequence at different temperatures are performed.At low temperatures (293 and 303K) the conformational stability of apoA is more pronounced compared to apoB adenine riboswitch.Thermal stability of apoA compared to apoB adenine riboswitch is the least at 323K temperature.At higher temperature (373K) and lower temperature (283K) apoA adenine riboswitch exerts moderate conformational stability.The nucleotides from stem2 and junction (J<sub>1/2</sub>, J<sub>2/3</sub>) regions of adenine riboswitch contribute the most to the conformational stability and order. Molecular Dynamics Simulation of ligand unbound two different conformations of adenine riboswitch with the same sequence at different temperatures are performed. At low temperatures (293 and 303K) the conformational stability of apoA is more pronounced compared to apoB adenine riboswitch. Thermal stability of apoA compared to apoB adenine riboswitch is the least at 323K temperature. At higher temperature (373K) and lower temperature (283K) apoA adenine riboswitch exerts moderate conformational stability. The nucleotides from stem2 and junction (J<sub>1/2</sub>, J<sub>2/3</sub>) regions of adenine riboswitch contribute the most to the conformational stability and order.