Salt bridges are formed by the attraction between positively and negatively charged amino acid side chains in proteins and play an important role in stabilizing protein structure, regulating enzyme activity, and mediating protein interactions. In proteins, salt bridges affect the functional and physicochemical properties of proteins, such as enzyme catalysis, protein-protein interactions, protein-DNA/RNA interactions, and molecular recognition. At CD ComputaBio, we offer comprehensive computational techniques, offers a comprehensive salt bridge analysis service designed to unravel the complex mechanisms and properties of salt bridges in complex biomass.
Our Algorithm
Molecular Dynamics Simulation (MD)
Molecular dynamics simulations allow the motion of atoms and molecules to be tracked in order to explore the formation, stability, and kinetic behavior of salt bridges.
Quantum Chemical Computational Methods
The use of quantum chemical methods (e.g., density functional theory) allows the energy, configuration, and electronic structure of salt bridge formation to be modeled and studied at the atomic level.
Protein conformational studies
Computational chemistry studies of the structure of proteins and protein complexes allow for the analysis of the role of salt bridges in protein stability and function.
Our Services
CD ComputaBio's salt bridge analysis service is designed to provide a comprehensive understanding of salt bridge dynamics and its impact on biomolecular systems. We carefully employ molecular dynamics simulations to study salt bridges' formation, stability, and contribution in proteins, protein-ligand complexes, and other macromolecular systems. The services we offer include:
Service for Identifying Salt Bridges
Salt Bridge Identification Service: We can identify and characterize salt bridges in biomolecular structures and thus map their spatial distribution in detail. This initial step lays the foundation for further analysis.
Salt Bridge Interaction Simulation Service: We utilize molecular dynamics (MD) and flow MD (FMD) simulations to study salt bridge interactions in proteins.
Description of Salt Bridge Dynamic Behavior: We describe the dynamic behavior of salt bridges and discuss the relationship between salt bridge interactions and local structure.
Salt Bridge Dynamics Service
Our simulations provide insight into the dynamic behavior of salt bridges over time, elucidating their propensity to form, break up, and remodel. By capturing the fluctuating properties of salt bridges, we gain insight into the flexibility and adaptability of salt bridges in the system.
Salt Bridge Stability and Energetics Services
- Stability Analysis Service: We analyze the stability of individual salt bridges and elucidate their contribution to the overall structural stability of the system. This analysis helps to understand the energetics of salt bridge interactions.
- Functional Characterization Service: Through this analysis, we strive to elucidate how salt bridges affect the functional properties of proteins, such as enzymatic activity, ligand binding, and structural
Delivery of Results
Upon completion of the salt bridge analysis, our clients receive a comprehensive and detailed report summarizing the results and insights from the molecular dynamics simulation. The report includes
- Salt Bridge Visualization
Workflow of Our Services
CD ComputaBio is dedicated to unraveling the intricate details of salt bridges within biomolecular systems, providing crucial insights into their dynamics, stability, and functional relevance. By leveraging the power of molecular dynamics simulations and state-of-the-art computational tools, we equip researchers and organizations with valuable data that shapes the understanding of complex molecular interactions and informs the development of innovative solutions in drug discovery and protein engineering.
References:
- Pacheco S, Gómez I, Sánchez J, et al. Helix α-3 inter-molecular salt bridges and conformational changes are essential for toxicity of Bacillus thuringiensis 3D-Cry toxin family. Scientific Reports, 2018, 8(1): 10331.
- Papaleo E, Renzetti G, Tiberti M. Mechanisms of intramolecular communication in a hyperthermophilic acylaminoacyl peptidase: a molecular dynamics investigation. PLoS One, 2012, 7(4): e35686.
- Basu S, Mukharjee D. Salt-bridge networks within globular and disordered proteins: characterizing trends for designable interactions. Journal of Molecular Modeling, 2017, 23: 1-17.
* For Research Use Only.
