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Salt Bridge Simulation


Salt bridge refers to a strong electrostatic interaction between positive and negative charges that binds two atomic groups together. It is generally a combination of two non-covalent interactions: hydrogen bonding and electrostatic interaction. Although non-covalent interaction is a relatively weak interaction, it plays an important role in the overall stability of the conformer when these weak interactions are superimposed together. Not only salt bridges are found in proteins, but also in supramolecular chemistry. Salt bridge in proteins is a bond between oppositely charged residues that are very close to each other and it helps to form a specific interactions between the protein and other biomolecules without increasing the free folding energy of the protein. In proteins, salt bridges affect the function and physical and chemical properties of proteins, such as enzyme catalysis, protein-protein interactions, protein-DNA/RNA interactions, molecular recognition, etc. Salt bridge interaction is also one of the most important electrostatic interactions to stabilize the secondary and tertiary structures of protein. In order to obtain more insight into the molecular basis of proteins, scientists often apply simulation method to evaluate the free energy contribution of salt bridges to the total free energy of the state and study the salt bridge networks.

Molecular dynamics simulation studies of the salt bridge between ArgIII:26 of the DRY motif at the intracellular end of TM-III and GluVI:-06 at the intracellular extension of TM-VI in B2AR.Figure 1. Molecular dynamics simulation studies of the salt bridge between ArgIII:26 of the DRY motif at the intracellular end of TM-III and GluVI:-06 at the intracellular extension of TM-VI in B2AR. (Valentin-Hansen, L.; et al. 2012)

Our Services

At Alfa Chemistry, we have rich experience in performing molecular dynamics simulation, flow molecular dynamics and accelerated sampling technique to study the salt bridge. Our fast and high-quality services include the following:

  • Our scientists can perform molecular dynamics simulations for conformational behavior, investigate the salt bridges and calculate the binding free energy.

  • We use molecular dynamics simulation technique to establish an optimized pH titration method. The strength of the salt bridge under different temperature conditions can be measured, and change of free energy of salt bridge with temperature is calculated either. In addition, our groups further study the formation mechanism of the salt bridge.

  • Our groups perform salt bridge analysis of the binding domain. We study a salt bridge interaction associated with the ligand and the surrounding protein residues. We also simulate salt bridge changes in the complex during the simulation in different temperature ranges.

  • We employ both molecular dynamics (MD) and Flow MD (FMD) simulations to investigate the salt bridges interactions of protein. The dynamic behaviors of salt bridges are characterized and the relation between salt bridge interactions and local structures are also discussed.

  • Our teams have applied a novel accelerated sampling technique to simulate and calculate salt bridge free energy surfaces in water. Moreover, our simulation results have been confirmed with NMR experiments.

  • Alfa Chemistry can also study mixed-salt effects on the conformation of a short salt-bridge-forming α helix, helping you to choose suitable inorganic salts.

What Our Simulations Offer?

  • Binding free energies
  • Salt bridging strength
  • Hydration of the salt bridges
  • Formation mechanism of the salt bridge

Why Choose Us?

  • At Alfa Chemistry, we are capable of providing more insight into protein-protein interaction by conducting salt bridge simulation.
  • We can use important data obtained from the salt bridge simulation to study the interaction mechanism of the ligand-receptor complex system.

Salt bridge simulation provides an effective way to optimize the chemical process. Our salt bridge simulation services remarkably reduce the cost, promote further experiments, and enhance the understanding of chemical process for customers worldwide. Our personalized and all-around services will satisfy your innovative study demands. If you are interested in our services, please don't hesitate to contact us. We are glad to cooperate with you and witness your success!


  • Valentin-Hansen, L.; et al. The Arginine of the DRY Motif in Transmembrane Segment III Functions as a Balancing Micro-switch in the Activation of the 2-Adrenergic Receptor. Journal of Biological Chemistry. 2012, 287(38): 31973-31982.

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