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Variation of folded polypeptide surface area with probe size.
1Biomolecular Modelling Laboratory, Imperial Cancer Research Fund Laboratories, Lincoln's Inn Fields, London, England.
Proteins
|January 1, 1991
Summary
Polypeptide surface area calculations reveal that contact, accessible, and molecular surface areas are probe-size dependent. Fractal dimensions of protein surfaces show significant probe size influence.
Area of Science:
- Biophysics
- Computational Biology
- Protein Structure Analysis
Background:
- Understanding protein surface area is crucial for predicting protein function and interactions.
- Previous studies have explored various methods for calculating protein surface area, but probe size dependency requires further investigation.
Purpose of the Study:
- To investigate the relationship between polypeptide surface area types (contact, accessible, molecular) and probe sphere radius.
- To analyze the fractal dimensions of protein surfaces and their dependence on probe size.
Main Methods:
- Calculated three types of polypeptide surface area (contact, accessible, molecular) using varying probe sphere radii.
- Analyzed surface areas of alpha-helices (myoglobin, leghemoglobin, polyalanine) and whole globins (myoglobin, leghemoglobin).
- Computed fractal dimensions for contact and molecular surfaces of helices and globins.
Main Results:
- Globin helices and globins exhibited similar surface area trends with changing probe size.
- Polyalanine helix surface area was smaller but showed a similar shape to globin helix areas.
- Fractal dimensions were highly dependent on probe size, with contact fractal dimension peaking at larger probe sizes.
Conclusions:
- Polypeptide surface area is significantly influenced by the probe sphere size used for mapping.
- Fractal analysis provides insights into the complex topography of protein surfaces.
- Most residues do not contribute to contact surfaces with large probes, indicating localized interactions.