Related Experiment Video
Updated: Sep 1, 2025
08:09
15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the µs-ms Timescale
Published on: April 19, 2021
5.3K
Microsecond MD Simulations of the Plexin-B1 RBD: 2. N-H Probability Densities and Conformational Entropy in
Netanel Mendelman1, Yaron Pshetitsky1, Zhenlu Li2
1The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel.
The Journal of Physical Chemistry. B
|August 17, 2022
Summary
This study reveals how Rac1 binding impacts protein structural flexibility, showing increased rigidity in key loops and turns. This binding contributes unfavorably to the free energy, unlike dimerization which has a favorable entropic contribution.
Area of Science:
- Structural Biology
- Computational Biophysics
- Protein Dynamics
Background:
- Protein flexibility is crucial for biological function and can be quantified using orientational probability densities (P_eq) of bond vectors.
- Conformational entropy (S) derived from P_eq provides insights into the entropic contribution to free energy changes in biological processes.
- The Rho GTPase binding domain (RBD) of Plexin-B1 plays a role in cellular signaling and undergoes conformational changes upon binding to GTPases.
Purpose of the Study:
- To develop and apply a novel method for deriving protein orientational probability densities (P_eq) and conformational entropy (S) from molecular dynamics (MD) simulations.
- To investigate the impact of small GTPase Rac1 binding on the structural flexibility of the Plexin-B1 RBD.
- To compare the effects of Rac1 binding with previously studied RBD dimerization on protein flexibility and entropic contributions.
Main Methods:
- Utilized a new method employing N-H bonds as probes to derive P_eq and S from 1 μs MD simulations.
- Analyzed changes in loop and turn flexibility within the RBD upon binding to Rac1.
- Quantified the entropic contribution of N-H bonds to the free energy of RBD-Rac1 binding and RBD dimerization.
Main Results:
- RBD-Rac1 binding increased rigidity in loops L1, L3, and L4, while enhancing flexibility in turns β2/α1 and α2/β5.
- RBD dimerization, in contrast, increased rigidity in L4 and flexibility in α-helices, β-strands, and L2.
- RBD-Rac1 binding resulted in an unfavorable entropic contribution of (5.9 ± 0.9) kJ/mol, whereas RBD dimerization yielded a favorable contribution of (-7.0 ± 0.7) kJ/mol.
Conclusions:
- Rac1 binding significantly alters the flexibility profile of the Plexin-B1 RBD, impacting specific loops and turns differently than dimerization.
- The observed rigidity of L1 upon Rac1 binding correlates with previously identified L1-L3 contacts.
- The study provides a new perspective on GTPase binding effects on protein dynamics and highlights distinct entropic contributions to binding and dimerization.
