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[Roughness of the globular protein surface]
I N Serdiuk1, O V Galzitskaia, A A Timchenko
1Institute of Protein Research, Russian Acad. Sci., Pushchino, Moscow Region.
Biofizika
|March 7, 1998
Summary
Globular protein size and asymmetry are independent of molecular mass. However, accessible surface area scaling suggests unique protein surface structures, requiring further investigation.
Area of Science:
- Biophysics
- Structural Biology
- Protein Science
Context:
- Low-resolution X-ray crystallography data provides insights into protein structures.
- Understanding protein size, volume, and surface area scaling is crucial for predicting protein behavior and function.
- Previous studies established scaling relationships for isometric bodies.
Purpose:
- To calculate the area and volume of approximating ellipsoids for 65 globular proteins using X-ray data.
- To investigate the relationship between protein molecular mass and its physical dimensions.
- To analyze the accessible surface area scaling with molecular mass and compare it to isometric bodies.
Summary:
- Calculations for 65 globular proteins show that their volume and area, derived from low-resolution X-ray data, scale similarly to isometric bodies with increasing molecular mass.
- This implies that globular protein asymmetry does not increase with size.
- A distinct scaling exponent (0.73) was observed for accessible surface area versus molecular mass, deviating from the expected 0.67 for isometric shapes.
- Spherical harmonics analysis ruled out domain organization as the cause for this deviation, pointing to surface structure peculiarities.
Impact:
- The findings suggest that globular proteins maintain a consistent asymmetry regardless of size.
- The observed deviation in accessible surface area scaling highlights unique characteristics of protein surfaces.
- Further detailed analysis of protein surface structure is warranted to fully explain these observations.