Macromolecular-macromolecule Interaction
Understanding macromolecular interactions is critical for unraveling biological processes, designing effective therapies, and optimizing protein engineering. Determining these interactions experimentally is challenging, time-consuming, and costly. Computational methods such as molecular dynamics simulations have emerged as powerful tools to complement experimental studies.CD ComputaBio can provide a variety of algorithms to observe the motion and interactions of atoms and molecules in macromolecular interactions over time, allowing us to observe and analyze the dynamic behavior of macromolecules at the atomic level.
Our Algorithm
Enhanced Sampling Methods
We employ advanced enhanced sampling techniques, such as metadynamics and replica-exchange MD, to overcome sampling limitations and efficiently explore the conformational space of macromolecules-macromolecules interactions.
Force Field Development
We utilize specialized force fields tailored for various macromolecules-macromolecules interactions, including proteins, peptides, and enzymes. These force fields accurately capture the interactions and dynamics, ensuring reliable simulations and analysis.
Binding Free Energy Calculations
CD ComputaBio employs rigorous methods, such as MM/PBSA and MM/GBSA, to calculate accurate binding free energies. These calculations provide quantitative insights into the binding affinities and can be used for virtual screening and lead optimization.
Our Services
CD ComputaBio offers a comprehensive range of molecular dynamics simulation services tailored to meet your specific research goals.
Protein-Protein Interactions
Protein-protein interactions: We provide molecular dynamics simulations that can reveal the interaction mechanisms between proteins, which can be used to study protein-protein binding processes and analyze proteins' roles in complexes.
Protein Function Prediction: By simulating the dynamic behavior of proteins, we can discover their possible functional sites and thus predict the biological functions of proteins.
Protein-Peptide Interactions
Alanine Scanning Mutagenesis: Through computational alanine scanning, we identify key residues crucial for protein-peptide interactions, enabling the rational design of peptide mimetics and inhibitors.
Binding Affinity Prediction: We employ advanced computational models to predict the binding affinity between proteins and peptides, providing valuable insights for drug development and lead optimization.
Protein-Enzyme Interactions
Protein Engineering and Design: We assist in the engineering and design of enzymes for tailored functionalities by employing computational tools to modify active sites, improve catalytic efficiency, and optimize substrate specificity.
Biofunctional Studies: Through protein-enzyme interaction analysis, we have gained a detailed understanding of the conformational changes during protein-enzyme interactions, thus revealing their biological significance.
Delivery of Results
We prioritize delivering comprehensive, high-quality results for our clients. Our services are tailored to specific research objectives and we provide detailed reports summarizing the results of each study. Our results include:
- Interaction Results Analysis
- Thermodynamics Results Analysis
- Conformational Changes Results Analysis
Workflow of Our Services
CD ComputaBio utilizes state-of-the-art tools, algorithms, and expertise to provide comprehensive services for macromolecule-macromolecule interactions. By utilizing MD simulations, we provide insight into protein-protein interactions, protein-peptide interactions, and protein-enzyme interactions. Our services contribute to drug discovery, protein engineering, and basic biology research, helping scientists gain a deeper understanding of macromolecular interactions. Contact us today to start your project.
Reference:
- Zheng C, Liu Y, Sun F, et al. Predicting protein–protein interactions between rice and blast fungus using structure-based approaches[J]. Frontiers in Plant Science, 2021, 12: 690124.
- Rodriguez-Abetxuko A, Sánchez-deAlcázar D, Muñumer P, et al. Tunable polymeric scaffolds for enzyme immobilization[J]. Frontiers in Bioengineering and Biotechnology, 2020, 8: 830.
- Voulgaridou G P, Theologidis V, Xanthis V, et al. Identification of a peptide ligand for human ALDH3A1 through peptide phage display: Prediction and characterization of protein interaction sites and inhibition of ALDH3A1 enzymatic activity[J]. Frontiers in Molecular Biosciences, 2023, 10: 1161111.
* For Research Use Only.
