Molecular Dynamics Simulations of Pentapeptides at Interfaces:  Salt Bridge and Cation−π Interactions†

Biochemistry ◽  
2003 ◽  
Vol 42 (30) ◽  
pp. 8976-8987 ◽  
Author(s):  
Marcela P. Aliste ◽  
Justin L. MacCallum ◽  
D. Peter Tieleman
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Salt Bridge ◽  
Π Interactions ◽  
Dynamics Simulations

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.

Solvation of diclofenac in water from atomistic molecular dynamics simulations – interplay between solute–solute and solute–solvent interactions

2018 ◽  
Vol 20 (13) ◽  
pp. 8629-8639 ◽  
Author(s):  
Mariana Kozlowska ◽  
Pawel Rodziewicz ◽  
Tillmann Utesch ◽  
Maria Andrea Mroginski ◽  
Anna Kaczmarek-Kedziera
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Molecular Dynamics Simulations ◽  
Aqueous Solubility ◽  
Solvent Interactions ◽  
Π Interactions ◽  
Self Association ◽  
Dynamics Simulations

Self-association of diclofenac in water via π–π interactions and C–H⋯π hydrogen bonds as a reason for its low aqueous solubility.

Molecular dynamics simulations reveal the mechanism of graphene oxide nanosheet inhibition of Aβ1–42 peptide aggregation

2019 ◽  
Vol 21 (21) ◽  
pp. 10981-10991 ◽  
Author(s):  
Yibo Jin ◽  
Yunxiang Sun ◽  
Yujie Chen ◽  
Jiangtao Lei ◽  
Guanghong Wei
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Graphene Oxide ◽  
Molecular Dynamics Simulations ◽  
Salt Bridge ◽  
Graphene Oxide Nanosheets ◽  
Peptide Interactions ◽  
Graphene Oxide Nanosheet ◽  
Dynamics Simulations ◽  
Β Sheet

Graphene oxide nanosheets inhibit Aβ1–42 aggregation by weakening inter-peptide interactions and reducing β-sheet contents mostly via salt bridge, hydrogen bonding and cation–π interactions with charged residues.

scholarly journals Phosphorylation of interfacial phosphosite leads to increased binding of Rap-Raf complex

2021 ◽  
Author(s):  
Devanand T ◽  
Susmita Ghosh ◽  
Prasanna Venkatraman ◽  
Satyavani Vemparala
Keyword(s):  
Molecular Dynamics ◽  
Network Analysis ◽  
Molecular Dynamics Simulations ◽  
Charge Distribution ◽  
Electrostatic Interactions ◽  
Salt Bridge ◽  
Complex Stability ◽  
Serine Residue ◽  
Entire Region ◽  
Dynamics Simulations

The effect of phosphorylation of a serine residue in the Rap protein, residing at the complex interface of Rap-Raf complex is studied using atomistic molecular dynamics simulations. As the phosphosite of interest (SER39) is buried at the interface of the Rap-Raf complex, phosphorylation of only Rap protein was simulated and then complexed with the RBD of Raf for further analysis of complex stability. Our simulations reveal that the phosophorylation increases the binding of complex through strong electrostatic interactions and changes the charge distribution of the interface significantly. This is manifested as an increase in stable salt-bridge interactions between the Rap and Raf of the complex. Network analysis clearly shows that the phosphorylation of SER39 reorganizes the community network to include the entire region of Raf chain, including, Raf L4 loop potentially affecting downstream signalling.

Variation in aspects of cysteine proteinase catalytic mechanism deduced by spectroscopic observation of dithioester intermediates, kinetic analysis and molecular dynamics simulations

2001 ◽  
Vol 357 (2) ◽  
pp. 343-352 ◽  
Author(s):  
James D. REID ◽  
Syeed HUSSAIN ◽  
Suneal K. SREEDHARAN ◽  
Tamara S. F. BAILEY ◽  
Surapong PINITGLANG ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Steady State ◽  
Molecular Dynamics Simulations ◽  
Large Scale ◽  
Catalytic Mechanism ◽  
Cysteine Proteinase ◽  
Salt Bridge ◽  
Dynamics Simulation ◽  
Active Centre ◽  
Dynamics Simulations

The possibility of a slow post-acylation conformational change during catalysis by cysteine proteinases was investigated by using a new chromogenic substrate, N-acetyl-Phe-Gly methyl thionoester, four natural variants (papain, caricain, actinidin and ficin), and stopped-flow spectral analysis to monitor the pre-steady state formation of the dithioacylenzyme intermediates and their steady state hydrolysis. The predicted reversibility of acylation was demonstrated kinetically for actinidin and ficin, but not for papain or caricain. This difference between actinidin and papain was investigated by modelling using QUANTA and CHARMM. The weaker binding of hydrophobic substrates, including the new thionoester, by actinidin than by papain may not be due to the well-known difference in their S2-subsites, whereby that of actinidin in the free enzyme is shorter due to the presence of Met211. Molecular dynamics simulation suggests that during substrate binding the sidechain of Met211 moves to allow full access of a Phe sidechain to the S2-subsite. The highly anionic surface of actinidin may contribute to the specificity difference between papain and actinidin. During subsequent molecular dynamics simulations the P1 product, methanol, diffuses rapidly (over < 8ps) out of papain and caricain but ‘lingers’ around the active centre of actinidin. Uniquely in actinidin, an Asp142–Lys145 salt bridge allows formation of a cavity which appears to constrain diffusion of the methanol away from the catalytic site. The cavity then undergoes large scale movements (over 4.8 Å) in a highly correlated manner, thus controlling the motions of the methanol molecule. The changes in this cavity that release the methanol might be those deduced kinetically.

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