scholarly journals TRPV1 activation relies on hydration/dehydration of nonpolar cavities

2017 ◽  
Author(s):  
Marina A. Kasimova ◽  
Aysenur Yazici ◽  
Yevgen Yudin ◽  
Daniele Granata ◽  
Michael L. Klein ◽  
...  

ABSTRACTTRPV1 promotes cationic currents across cellular membranes in response to multiple stimuli such as increased temperature, binding of chemicals, low pH and voltage. The molecular underpinnings of TRPV1 gating, in particular the mechanism of temperature sensitivity, are still largely unknown. Here, we used molecular simulations and electrophysiology to shed light on the closed to open transition. Specifically, we found that gating of TRPV1 relies on the motion of an evolutionarily conserved amino acid (N676) in the middle of the S6 helix. On rotation, the side chain of this asparagine faces either the central pore or the S4-S5 linker. Only in the former case is the central pore hydrated and thus conductive. Interestingly, when N676 rotates toward the linker, we observe hydration of four so far unreported small nonpolar cavities. Based on these findings, we propose a model for TRPV1 gating involving the dynamic hydration of these four cavities. Free energy calculations indicate that this gating mechanisms is markedly temperature dependent favoring the open state at high temperature. On the basis of this model, which is able to rationalize a wealth of seemingly conflicting and/or unrelated experimental observations, we predicted the behavior of two single residue mutants, M572A and F580Y, the consequences of which we confirmed experimentally.

2016 ◽  
Vol 94 (2) ◽  
pp. 147-158 ◽  
Author(s):  
Huiqun Wang ◽  
Wei Cui ◽  
Chenchen Guo ◽  
Bo-Zhen Chen ◽  
Mingjuan Ji

NS5B polymerase plays an important role in viral replication machinery. TMC647055 (TMC) is a novel and potent non-nucleoside inhibitor of the HCV NS5B polymerase. However, mutations that result in drug resistance to TMC have been reported. In this study, we used molecular dynamics (MD) simulations, binding free energy calculations, and free energy decomposition to investigate the drug resistance mechanism of HCV to TMC resulting from L392I, P495T, P495S, and P495L mutations in NS5B polymerase. From the calculated results we determined that the decrease in the binding affinity between TMC and NS5BL392I polymerase is mainly caused by the extra methyl group at the CB atom of Ile. The polarity of the side-chain of residue 495 has no distinct influence on residue 495 binding with TMC, whereas the smaller size of the side-chain of residue 495 causes a substantial decrease in the van der Walls interaction between TMC and residue 495. Moreover, the longer length of the side-chain of residue 495 has a significant effect on the electrostatic interaction between TMC and Arg-503. Finally, we performed the same calculations and detailed analysis on other 3 mutations (L392V, P495V, and P495I). The results further confirmed our conclusions. The computational results not only reveal the drug resistance mechanism between TMC647055 and NS5B polymerase, but also provide valuable information for the rational design of more potent non-nucleoside inhibitors targeting HCV NS5B polymerase.


2014 ◽  
Vol 29 (08) ◽  
pp. 1450043 ◽  
Author(s):  
Rui-Hui Lin ◽  
Xiang-Hua Zhai

We reconsider the thermal scalar Casimir effect for p-dimensional rectangular cavity inside (D+1)-dimensional Minkowski space–time and clarify the ambiguity in the regularization of the temperature-dependent part of the free energy. We derive rigorously the regularization of the temperature-dependent part of the free energy by making use of the Abel–Plana formula repeatedly and get the explicit expression of the terms to be subtracted. In the cases of D = 3, p = 1 and D = 3, p = 3, we precisely recover the results of parallel plates and three-dimensional box in the literature. Furthermore, for D>p and D = p cases with periodic, Dirichlet and Neumann boundary conditions, we give the explicit expressions of the Casimir free energy in both low temperature (small separations) and high temperature (large separations) regimes, through which the asymptotic behavior of the free energy changing with temperature and the side length is easy to see. We find that for D>p, with the side length going to infinity, the Casimir free energy tends to positive or negative constants or zero, depending on the boundary conditions. But for D = p, the leading term of the Casimir free energy for all three boundary conditions is a logarithmic function of the side length. We also discuss the thermal Casimir force changing with temperature and the side length in different cases and find that when the side length goes to infinity, the force always tends to be zero for different boundary conditions regardless of D>p or D = p. The Casimir free energy and force at high temperature limit behave asymptotically alike that they are proportional to the temperature, be they positive (repulsive) or negative (attractive) in different cases. Our study may be helpful in providing a comprehensive and complete understanding of this old problem.


2020 ◽  
Author(s):  
Hannah Baumann ◽  
Vytautas Gapsys ◽  
Bert L. de Groot ◽  
David Mobley

<div>Binding free energy calculations have become increasingly valuable to drive decision making in drug discovery projects. </div><div>However, among other issues, inadequate sampling can reduce accuracy, limiting the value of the technique.</div><div>In this paper we apply absolute binding free energy calculations to ligands binding to T4 lysozyme L99A and HSP90 using equilibrium and non-equilibrium approaches. We highlight sampling problems encountered in these systems, such as slow side chain rearrangements and slow changes of water placement upon ligand binding. These same types of challenges are likely to show up in other protein-ligand systems as well and we propose some strategies to diagnose and test for such problems in alchemical free energy calculations. We also explore similarities and differences in how the equilibrium and the non-equilibrium approaches handle these problems. Our results show the large amount of work still to be done to make free energy calculations robust and reliable and provide insight for future research in this area. </div>


2012 ◽  
Vol 86 (5) ◽  
Author(s):  
Nikolas Antolin ◽  
Oscar D. Restrepo ◽  
Wolfgang Windl

2021 ◽  
Author(s):  
Hannah Baumann ◽  
Vytautas Gapsys ◽  
Bert L. de Groot ◽  
David Mobley

<div>Binding free energy calculations have become increasingly valuable to drive decision making in drug discovery projects. </div><div>However, among other issues, inadequate sampling can reduce accuracy, limiting the value of the technique.</div><div>In this paper we apply absolute binding free energy calculations to ligands binding to T4 lysozyme L99A and HSP90 using equilibrium and non-equilibrium approaches. We highlight sampling problems encountered in these systems, such as slow side chain rearrangements and slow changes of water placement upon ligand binding. These same types of challenges are likely to show up in other protein-ligand systems as well and we propose some strategies to diagnose and test for such problems in alchemical free energy calculations. We also explore similarities and differences in how the equilibrium and the non-equilibrium approaches handle these problems. Our results show the large amount of work still to be done to make free energy calculations robust and reliable and provide insight for future research in this area. </div>


2020 ◽  
Author(s):  
Hannah Baumann ◽  
Vytautas Gapsys ◽  
Bert L. de Groot ◽  
David Mobley

<div>Binding free energy calculations have become increasingly valuable to drive decision making in drug discovery projects. </div><div>However, among other issues, inadequate sampling can reduce accuracy, limiting the value of the technique.</div><div>In this paper we apply absolute binding free energy calculations to ligands binding to T4 lysozyme L99A and HSP90 using equilibrium and non-equilibrium approaches. We highlight sampling problems encountered in these systems, such as slow side chain rearrangements and slow changes of water placement upon ligand binding. These same types of challenges are likely to show up in other protein-ligand systems as well and we propose some strategies to diagnose and test for such problems in alchemical free energy calculations. We also explore similarities and differences in how the equilibrium and the non-equilibrium approaches handle these problems. Our results show the large amount of work still to be done to make free energy calculations robust and reliable and provide insight for future research in this area. </div>


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