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

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4967 ◽  
Author(s):  
Mustapha Carab Ahmed ◽  
Elena Papaleo ◽  
Kresten Lindorff-Larsen
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Force Fields ◽  
Salt Bridge ◽  
Dynamics Simulation ◽  
Ionic Interactions ◽  
Salt Bridges ◽  
Important Interaction ◽  
The Stability ◽  
Dynamics Simulations

Salt 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 simulation 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 depends 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 lysine-carboxylate 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 overestimated, to different extents, in simulations of GB1 using seven out of eight commonly used combinations of fixed charge force fields and water models. We also find that the Amber ff15ipq force field gives rise to weaker salt bridges in good agreement with the NMR experiments. We conclude that many force fields appear to overstabilize these ionic interactions, and that further work may be needed to refine our ability to model quantitatively the stability of salt bridges through simulations. We also suggest that comparisons between NMR experiments and simulations will play a crucial role in furthering our understanding of this important interaction.

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.

Investigation on salt bridge interactions of mammalian prion proteins by molecular dynamics simulation / Memeli prion proteinlerinin moleküler dinamik simulasyon ile tuz köprüleri etkileşimlerinin araştırılması

2016 ◽  
Vol 41 (3) ◽  
Author(s):  
Xiliang Chen ◽  
Xin Chen ◽  
Yafang Liu
Keyword(s):  
Molecular Dynamics ◽  
Prion Protein ◽  
Electrostatic Interactions ◽  
Prion Proteins ◽  
Salt Bridge ◽  
Dynamics Simulation ◽  
Salt Bridges ◽  
Tertiary Structures ◽  
Local Structures ◽  
The Stability

AbstractObjective: Salt bridge interaction is one of the most important electrostatic interactions to stabilize the secondary and tertiary structures of protein. To obtain more insight into the molecular basis of prion proteins, the salt bridge networks in two animal prion proteins are studied in this work.Methods: Molecular dynamics (MD) and Flow MD (FMD) simulations are employed to investigate the salt bridges interactions of rabbit prion protein (rPrPc), Syrian hamster prion protein (syPrPc) and the variants of the two prion proteins.Results: The dynamic behaviors of salt bridges are characterized, and the relation between salt bridge interactions and local structures are also discussed. The type of salt bridges in the two prion proteins is divided into the helixloop, intra-helix and inter-helix salt bridges. It is found that the helix-loop salt bridges is more important for the stability of prion proteins than the other two kinds of slat bridge.Conclusion: The Asp201-Arg155 (rS1), Asp177-Arg163 (rS3) and Asp178-Arg164 (syS1) are the important salt bridges to stabilize the structures of rPrPc and syPrPc, respectively. The structural stability is partly depended on the number of helix-loop salt bridge.

Exploring Cyclodextrin Glycosyltransferase's Thermostability through Molecular Dynamics Simulation

2013 ◽  
Vol 647 ◽  
pp. 434-437 ◽  
Author(s):  
Yi Fu ◽  
Qi Fang Gu
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Working Conditions ◽  
Thermal Stabilization ◽  
Salt Bridge ◽  
Dynamics Simulation ◽  
Salt Bridges ◽  
Cyclodextrin Glycosyltransferase ◽  
Specific Knowledge ◽  
Dynamics Simulations

Cyclodextrin glycosyltransferase (EC 2.4.1.19, CGTase) is an important industrial enzyme in the production of cyclodextrins. However, the working conditions are extreme, which often restrict the usage of CGTase. Thermal stability is of great importance for this enzyme. Besides to screen microorganism for CGTase that fit the requirement of biotechnology, it is also hoped that protein engineering can tailor CGTase to meet demands of industry. In this work, molecular dynamics simulations were performed to study thermal stabilization of CGTase C-terminal structured region. Dynamic motions of salt bridges in thermal unstable regions were monitored during the simulations. In the C-terminal region, salt bridge Arg591-Asp640 and Lys652-Glu664 were proposed to be more important for stability than the others. Sheet1 and Sheet3 through the Arg591-Asp640 salt-bridge formation renders the C-terminal stable. The salt bridge Lys652-Glu664 linking sheet4 and sheet5 terminal also contributes to the structural stability of C-terminal. This study is attempt to observe the dynamic behavior of CGTase C-terminal at high temperatures and to understand the factors conferring thermostability of this protein. The results provide specific knowledge about thermal stability in CGTase C-terminal and may help to design biotechnologically improved thermostable proteins.

scholarly journals Refining amino acid hydrophobicity for dynamics simulation of membrane proteins

2017 ◽  
Author(s):  
Ronald D Hills, Jr
Keyword(s):  
Molecular Dynamics ◽  
Membrane Proteins ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Interfacial Behavior ◽  
Potentials Of Mean Force ◽  
Arginine Residues ◽  
Dynamics Simulations

Coarse-grained simulations enable the study of membrane proteins in the context of their native environment but require reliable parameters. The CgProt force field is assessed by comparing the potentials of mean force for sidechain insertion in a DOPC bilayer to results reported for atomistic molecular dynamics simulations. The reassignment of polar sidechain sites was found to improve the attractive interfacial behavior of tyrosine, phenylalanine and asparagine as well as charged lysine and arginine residues. The solvation energy at membrane depths of 0, 1.3 and 1.7 nm correlate with experimental partition coefficients in aqueous mixtures of cyclohexane, octanol and POPC, respectively, for sidechain analogs and Wimley-White peptides. These data points can be used to further discriminate between alternate force field parameters. Available partitioning data was also used to reparameterize the representation of the polar peptide backbone for non-alanine residues. The newly developed force field, CgProt 2.4, correctly predicts the global energy minimum in the potentials of mean force for insertion of the uncharged membrane-associated peptides LS3 and WALP23. CgProt will find application in molecular dynamics simulations of a variety of membrane protein systems.

scholarly journals Quantifying the Strength of a Salt Bridge by Neutron Scattering and Molecular Dynamics

2019 ◽  
Author(s):  
Philip E. Mason ◽  
Pavel Jungwirth ◽  
Elise Duboué-Dijon
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Neutron Scattering ◽  
Salt Bridge ◽  
Ion Pairing ◽  
Structural Features ◽  
Quantitative Agreement ◽  
Salt Bridges ◽  
Hydrophobic Contact ◽  
Guanidinium Cation

The molecular structure and strength of a model salt bridge between a guanidinium cation as the charged side chain group of arginine and the carboxylic group of acetate in an aqueous solutions is characterized by a combination of neutron diffraction with isotopic substitution and molecular dynamics simulations. Being able to recover the second order difference signal, the present neutron scattering experiments provide direct information about ion pairing in the investigated solution. At the same time, these measurements serve as benchmarks for assessing the quality of the force field employed in the simulation. We show that a standard non-polarizable force field, which tends to overestimate the strength of salt bridges, does not reproduce the structural features from neutron scattering pertinent to ion pairing. In contrast, a quantitative agreement with experiment is obtained when electronic polarization effects are accounted for in a mean-field way via charge scaling. Such simulations are then used to quantify the weak character of a fully hydrated salt bridge. Finally, on top of the canonical hydrogen-bonding binding mode between guanidinium and acetate, these simulations also point to another interaction motif involving an out-of-plane hydrophobic contact of the methyl group of acetate with the guanidinium cation.

scholarly journals A molecular dynamics simulation study on the propensity of Asn-Gly-containing heptapeptides towards β-turn structures: Comparison with ab initio quantum mechanical calculations

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243429
Author(s):  
Dimitrios A. Mitsikas ◽  
Nicholas M. Glykos
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Quantum Mechanical ◽  
Type I ◽  
Quantum Mechanical Calculations ◽  
Water Solvent ◽  
Simulation Protocol ◽  
Dynamics Simulations

Both molecular mechanical and quantum mechanical calculations play an important role in describing the behavior and structure of molecules. In this work, we compare for the same peptide systems the results obtained from folding molecular dynamics simulations with previously reported results from quantum mechanical calculations. More specifically, three molecular dynamics simulations of 5 μs each in explicit water solvent were carried out for three Asn-Gly-containing heptapeptides, in order to study their folding and dynamics. Previous data, based on quantum mechanical calculations within the DFT framework have shown that these peptides adopt β-turn structures in aqueous solution, with type I’ β-turn being the most preferred motif. The results from our analyses indicate that at least for the given systems, force field and simulation protocol, the two methods diverge in their predictions. The possibility of a force field-dependent deficiency is examined as a possible source of the observed discrepancy.

scholarly journals Predicting NMR Relaxation of Proteins from Molecular Dynamics Simulations with Accurate Methyl Rotation Barriers

2020 ◽  
Author(s):  
Falk Hoffmann ◽  
Frans Mulder ◽  
Lars V. Schäfer
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Force Fields ◽  
Nmr Relaxation ◽  
Md Simulations ◽  
Quantitative Agreement ◽  
Relaxation Rates ◽  
Protein Force Fields ◽  
Dynamics Simulations ◽  
Methyl Rotation

The internal dynamics of proteins occurring on time scales from picoseconds to nanoseconds can be sensitively probed by nuclear magnetic resonance (NMR) spin relaxation experiments, as well as by molecular dynamics (MD) simulations. This complementarity offers unique opportunities, provided that the two methods are compared at a suitable level. Recently, several groups have used MD simulations to compute the spectral density of backbone and side-chain molecular motions, and to predict NMR relaxation rates from these. Unfortunately, in the case of methyl groups in protein side-chains, inaccurate energy barriers to methyl rotation were responsible for a systematic discrepancy in the computed relaxation rates, as demonstrated for the AMBER ff99SB*-ILDN force field (and related parameter sets), impairing quantitative agreement between simulations and experiments. However, correspondence could be regained by emending the MD force field with accurate coupled cluster quantum chemical calculations. Spurred by this positive result, we tested whether this approach could be generally applicable, in spite of the fact that different MD force fields employ different water models. Improved methyl group rotation barriers for the CHARMM36 and AMBER ff15ipq protein force fields were derived, such that the NMR relaxation data obtained from the MD simulations now also display very good agreement with experiment. Results herein showcase the performance of present-day MD force fields, and manifest their refined ability to accurately describe internal protein dynamics.

scholarly journals Quantifying the Strength of a Salt Bridge by Neutron Scattering and Molecular Dynamics

2019 ◽  
Author(s):  
Philip E. Mason ◽  
Pavel Jungwirth ◽  
Elise Duboué-Dijon
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Neutron Scattering ◽  
Salt Bridge ◽  
Ion Pairing ◽  
Structural Features ◽  
Quantitative Agreement ◽  
Salt Bridges ◽  
Hydrophobic Contact ◽  
Guanidinium Cation

The molecular structure and strength of a model salt bridge between a guanidinium cation as the charged side chain group of arginine and the carboxylic group of acetate in an aqueous solutions is characterized by a combination of neutron diffraction with isotopic substitution and molecular dynamics simulations. Being able to recover the second order difference signal, the present neutron scattering experiments provide direct information about ion pairing in the investigated solution. At the same time, these measurements serve as benchmarks for assessing the quality of the force field employed in the simulation. We show that a standard non-polarizable force field, which tends to overestimate the strength of salt bridges, does not reproduce the structural features from neutron scattering pertinent to ion pairing. In contrast, a quantitative agreement with experiment is obtained when electronic polarization effects are accounted for in a mean-field way via charge scaling. Such simulations are then used to quantify the weak character of a fully hydrated salt bridge. Finally, on top of the canonical hydrogen-bonding binding mode between guanidinium and acetate, these simulations also point to another interaction motif involving an out-of-plane hydrophobic contact of the methyl group of acetate with the guanidinium cation.

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