Foldamer Architectures of Triazine-Based Sequence-Defined Polymers Investigated with Molecular Dynamics Simulations and Enhanced Sampling Methods

2019 ◽  
Vol 123 (44) ◽  
pp. 9364-9377 ◽  
Author(s):  
Surl-Hee Ahn ◽  
Jay W. Grate
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Sampling Methods ◽  
Enhanced Sampling ◽  
Dynamics Simulations

scholarly journals Using Long-Timescale Molecular Dynamics Simulations to Benchmark Enhanced Sampling Methods

2015 ◽  
Vol 108 (2) ◽  
pp. 183a
Author(s):  
Albert C. Pan ◽  
Thomas M. Weinreich ◽  
Stefano Piana ◽  
David E. Shaw
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Sampling Methods ◽  
Enhanced Sampling ◽  
Dynamics Simulations

The shuttling mechanism of foldaxanes: more than just translocation and rotation

2020 ◽  
Vol 22 (23) ◽  
pp. 12967-12972
Author(s):  
Peng Liu ◽  
Wenqi Hao ◽  
Xihui Bian ◽  
Donghai Mei
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Sampling Methods ◽  
Molecular Machines ◽  
Enhanced Sampling ◽  
Shrinkage And Swelling ◽  
Dynamics Simulations

Understanding movements within molecular machines is the prerequisite of tailoring its structure to achieve specific functions. With the aid of molecular dynamics simulations and enhanced sampling methods, movements within the foldaxane have been revealed. Movements, viz., translocation, rotation, tilt, shrinkage, and swelling, have been identified and investigated in detail.

scholarly journals How well do force fields capture the strength of salt bridges in proteins?

2018 ◽  
Author(s):  
Mustapha Carab Ahmed ◽  
Elena Papaleo ◽  
Kresten Lindorff-Larsen
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Force Fields ◽  
Salt Bridge ◽  
Salt Bridges ◽  
Enhanced Sampling ◽  
Important Interaction ◽  
Close Proximity ◽  
The Stability ◽  
Dynamics Simulations

AbstractSalt bridges form between pairs of ionisable residues in close proximity and are important interactions in proteins. While salt bridges are known to be important both for protein stability, recognition and regulation, we still do not have fully accurate predictive models to assess the energetic contributions of salt bridges. Molecular dynamics simulations is one technique that may be used study the complex relationship between structure, solvation and energetics of salt bridges, but the accuracy of such simulations depend on the force field used. We have used NMR data on the B1 domain of protein G (GB1) to benchmark molecular dynamics simulations. Using enhanced sampling simulations, we calculated the free energy of forming a salt bridge for three possible ionic interactions in GB1. The NMR experiments showed that these interactions are either not formed, or only very weakly formed, in solution. In contrast, we show that the stability of the salt bridges is slightly overestimated in simulations of GB1 using six commonly used combinations of force fields and water models. We therefore conclude that further work is needed to refine our ability to model quantitatively the stability of salt bridges through simulations, and that comparisons between experiments and simulations will play a crucial role in furthering our understanding of this important interaction.

scholarly journals Ring Puckering Landscapes of Glycosaminoglycan-Related Monosaccharides from Molecular Dynamics Simulations

2019 ◽  
Author(s):  
Irfan Alibay ◽  
Richard Bryce
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Biological Function ◽  
Enhanced Sampling ◽  
Energy Profiles ◽  
Ring Puckering ◽  
Dynamics Simulations ◽  
Ring Pucker ◽  
Free Energy Profiles

<p>The conformational flexibility of the glycosaminoglycans (GAGs) are known to be key in their binding and biological function, for example in regulating coagulation and cell growth. In this work, we employ enhanced sampling molecular dynamics simulations to probe the ring conformations of GAG-related monosaccharides, including a range of acetylated and sulfated GAG residues. We first perform unbiased MD simulations of glucose anomers and the epimers glucoronate and iduronate. These calculations indicate that in some cases, an excess of 15 microseconds are required for adequate sampling of ring pucker due to the high energy barriers between states. However, by applying our recently developed msesMD simulation method (multidimensional swarm enhanced sampling molecular dynamics), we were able to quantitatively and rapidly reproduce these ring pucker landscapes. From msesMD simulations, the puckering free energy profiles were then compared for eleven monosaccharides found in GAGs; this includes to our knowledge the first simulation study of sulfation effects on GalNAc ring puckering. For the force field employed, we find that in general the calculated pucker free energy profiles for sulfated sugars were similar to the corresponding unsulfated profiles. This accords with recent experimental studies suggesting that variation in ring pucker of sulfated GAG residues is primarily dictated by interactions with surrounding residues rather than by intrinsic conformational preference. As an exception to this, however, we predict that 4-O-sulfation of GalNAc leads to reduced ring rigidity, with a significant lowering in energy of the <sup>1</sup>C<sub>4</sub> ring conformation; this observation may have implications for understanding the structural basis of the biological function of GalNAc-containing glycosaminoglycans such as dermatan sulfate.</p>

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