Salt-Bridge Analysis Service
Salt-bridge analysis is a method used to evaluate electrostatic interactions between charged amino acid residues in molecules, often employed to identify key linkages in protein structure and stability. CD ComputaBio employs MD simulations with polarizable force fields and free energy decomposition protocols to map salt-bridge lifetime distributions (τ > 500 ps) and pH-dependent protonation states.
Overview of Salt-Bridge
A salt bridge refers to a stabilizing electrostatic interaction between oppositely charged groups (e.g., carboxylate anions and protonated amines) within or between molecules. In biological systems, salt bridges play a critical role in maintaining protein structure and function-they stabilize tertiary/quaternary conformations, mediate ligand-receptor binding, and regulate enzymatic activity by fine-tuning active site chemistry. In drug design, engineering salt bridges can improve target specificity and pharmacokinetics by reducing off-target interactions.
Fig. 1 Molecular dynamics simulations analysis of GlacPETase and salt bridge mutants. (QI X, et al., 2024)
Methods of Salt Bridge Analysis
Salt bridge analysis is crucial in understanding the structural and functional aspects of biomolecules, particularly proteins and nucleic acids.
Computational Simulation Methods
- Molecular Dynamics (MD) Simulations
- Quantum Chemical Calculations
- Hybrid QM/MM Methods
- Electrostatic Surface Analysis
Experimental Biochemical Methods
- Site-Directed Mutagenesis
- Differential Scanning Calorimetry (DSC)
- Circular Dichroism (CD) Spectroscopy.
- Isothermal Titration Calorimetry (ITC)
Structural Biology Methods
- X-ray Crystallography
- Nuclear Magnetic Resonance (NMR) Spectroscopy
- Cryo-Electron Microscopy (Cryo-EM)
Bioinformatics and Computational Tools
- Salt Bridge Detection Software
- Database Analysis
- Sequence and Structure Prediction
Our Services
Utilizing advanced computational platforms and expert teams, CD ComputaBio offers salt-bridge analysis service to help clients thoroughly analyze the impact of electrostatic interactions on molecular structure and stability. Our services provide robust support for drug design and protein optimization, enabling clients to achieve precise regulation of molecular functions.
Salt Bridge Recognition and Interaction Analysis
Leveraging molecular dynamics simulations and electrostatic potential calculations, CD ComputaBio can accurately identify salt bridge sites within protein-ligand complexes. We analyze their contributions to binding stability and specificity, guiding molecular design and optimization efforts.
Salt Bridge Stability
Assessment
By combining free energy decomposition with monitoring of hydrogen bonds and electrostatic interactions, we quantitatively assess the energy contributions of salt bridges during dynamic binding processes. This provides data support for optimizing protein stability and drug efficacy.
Prediction of Salt Bridge Mutation Effects
Utilizing site-directed mutation simulations and binding free energy calculations, we predict the impact of mutations in key salt bridge residues on molecular interactions. This assists in studies of target resistance and functional site validation, informing more effective drug development strategies.
Applications of Salt Bridge Analysis in Molecular Structural Analysis
- Protein Molecular Structure Analysis
- Protein-Protein Interaction Analysis
- Enzyme-Substrate and Inhibitor Interaction Analysis
- Protein-Nucleic Acid Interaction Analysis
- Protein-Ligand Interaction Analysis
- Peptide and Short-Chain Protein Structural Analysis
- Protein-Small Molecule Interaction Analysis
- Protein Aggregation and Misfolding Analysis
- Nucleic Acid Structural Analysis
- More
CD ComputaBio boasts an outstanding research team specializing in salt-bridge analysis, offering comprehensive one-stop services. If you encounter any challenges in your project, please don't hesitate to contact us for expert assistance.
Reference:
- QI X, WU Y, ZHANG S T, et al. The unique salt bridge network in GlacPETase: a key to its stability [J]. Applied and environmental microbiology, 2024, 90(3): e0224223.
* For Research Use Only.
Related Services
