Solvent Accessible Surface Area (SASA) Analysis Services
Solvent accessible surface area (SASA) analysis is an important component of structural biology and biophysical chemistry. It provides an important basis for understanding the molecular interactions, stability and function of proteins, DNA and RNA. With a commitment to excellence, innovation and scientific acumen, CD ComputaBio has become a pioneer in providing advanced SASA analytical services to the scientific and pharmaceutical industries.
Introduction to SASA
Solvent accessible surface area (SASA) is a key parameter in molecular structure studies, which describes the region around a macromolecule that is accessible to solvent molecules. It is an important indicator for understanding protein folding, ligand binding, and conformational changes, and plays a key role in elucidating molecular interactions at the atomic level. Typically, SASA is used to predict how ligands or proteins interact with the aqueous environment and study protein folding, binding sites, and overall molecular dynamics.
Fig.1 Solvent accessible surface area (SASA) backbone atoms relative to the starting minimized structure over 300 ns. (Elamin G, et al.; 2022)
Application of SASA Analysis
- 1Protein Folding and Stability Characterization
- Hydrophobicity Assessment: During protein folding, hydrophobic residues tend to be buried within the protein core, thereby reducing their SASA, which helps improve protein stability. SASA analysis helps identify hydrophobic and hydrophilic regions in proteins.
- Mutation Effects Study: Compare the SASA of wild-type and mutants to understand the effects of mutations on structure and function.
- 2Binding Site Identification
- Active Site Characterization: SASA analysis can pinpoint exposed residues that may be involved in ligand binding or catalytic activity.
- Drug Design: Identification SASA can help target drug binding to specific regions, thereby improving the efficacy of drug candidates.
- 3Molecular Interaction Studies
- Interaction Surface Mapping: SASA helps determine the contact area between interacting proteins or between a protein and a ligand.
- Binding Affinity Estimation: Changes in SASA upon complex formation can be correlated to binding energy, helping to quantify the strength of an interaction.
- 4Molecular Dynamics and Simulation Studies
- Conformational Analysis: Monitoring SASA through simulation trajectories can reveal conformational changes and stability of biomolecules under different conditions.
- Simulating Molecular Interactions: In docking and molecular dynamics simulations, SASA is used to evaluate binding free energy and interaction strength.
Our Services
SASA analysis is a primary method for studying the behavior and function of biomolecules (such as proteins or nucleic acids) in solution by calculating their surface area in solution. The algorithm used by CD ComputaBio calculates the surface area of a molecule in solution by performing a fine-grained three-dimensional mesh of each atom of the molecule, including the solvent molecules surrounding it, and summing and integrating over them.
Our services include but are not limited to:
Protein SASA Calculation
Accurately determine the SASA of proteins, analyze the folding state, conformational changes, and surface properties of individual proteins, as well as study protein-protein interaction interfaces, and identify binding sites and interaction regions.
Small Molecule SASA Calculation
Accurately evaluate the SASA of small molecules, predict drug-target interactions, and evaluate their bioavailability and solubility.
Ligand SASA Calculation
Perform SASA calculations on individual ligand molecules and evaluate changes in their surface area exposed to solvent during binding to receptors, such as proteins and nucleic acids.
Nucleic Acid SASA Calculation
Accurately determine the SASA of nucleic acids and evaluate the structural stability, folding mode, and interaction of nucleic acids with proteins or small molecules.
Carbohydrate SASA Calculation
Accurately calculate the SASA of polysaccharides and oligosaccharides, study the structural characteristics of glycoproteins, glycolipids, etc., and analyze the effects of glycosylation on the molecular surface.
Complex SASA Calculations
Thoroughly analyze the SASA of protein-ligand complexes, protein-nucleic acid complexes, and enzyme-substrate complexes, and delve into binding interfaces and intermolecular interactions.
Tools for SASA Calculation
At CD ComputaBio, our experts perform SASA analysis using Amber, a state-of-the-art molecular simulation software. Cpptraj is a key program in Amber that processes and analyzes molecular dynamics trajectories and derives SASA-related datasets. Here, we provide two algorithms ( i.e., molsulf and surf) to interpret the molecular behavior in different states, such as intact proteins or certain protein residues.
Molsulf Analysis
- The Molsurf algorithm is widely recommended for accurately calculating and systematically comparing the solvent-accessible surface of entire protein structures.
- Molsurf precisely calculates the total exposed surface area of the object, which quantitatively equals the complete solvent-accessible surface of the entire protein macromolecule.
Surf Analysis
- When you want to obtain the SASA of a part or some residues of a protein, our scientists will use surf to assist you in calculating it.
- Surf can also roughly calculate the hydrophobic SASA and hydrophilic SASA if the corresponding hydrophobic residues and hydrophilic residues are specified.
CD ComputaBio's SASA analysis service can help you deeply understand the behavior of molecules in solvents and their functions in molecular interactions, providing accurate data to support your research. Our professional team provides you with the best service with a scientific attitude and rigorous method, and your satisfaction is our highest pursuit. contact us now for more details on our services!
References:
- Elamin G, et al. Multi-catalytic Sites Inhibition of Bcl2 Induces Expanding of Hydrophobic Groove: A New Avenue Towards Waldenström Macroglobulinemia Therapy. Protein J. 2022;41(2):201-215.
- Ali, SA; et al. A review of methods available to estimate solvent-accessible surface areas of soluble proteins in the folded and unfolded states. Curr Protein Pept Sci. 2014;15(5):456-476.
* For Research Use Only.
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