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Size-independent comparison of protein three-dimensional structures
1College of Pharmacy, University of Michigan, Ann Arbor 48109, USA.
Proteins
|July 1, 1995
Summary
A new measure, rho, offers a size-independent way to compare protein structures. This method helps determine true structural similarity beyond arbitrary root-mean-square deviation cutoffs, aiding in protein modeling and NMR structure determination.
Area of Science:
- Structural Biology
- Computational Biology
- Biophysics
Background:
- Protein structure comparison commonly uses root-mean-square deviation (RMSD), but its significance, especially above 2-3 Å, is unclear.
- Previous work suggested protein similarity cutoffs depend on chain length, lacking universality.
Purpose of the Study:
- Introduce a new, size-independent structural similarity measure, rho, based on RMSD.
- Establish universal cutoffs for protein structural similarity, independent of molecular size or properties.
Main Methods:
- Developed a new similarity metric, rho, based on RMSD.
- Scaled protein structures by radius of gyration and principal moments of inertia for universal comparison.
- Analyzed the distribution of rho values for random protein structures with increasing chain length.
Main Results:
- Visual similarity is recognized when rho < 0.4-0.5.
- An intrinsic cutoff of rho < 1.0 indicates overall folding motif similarity.
- Scaled comparisons eliminate size and ellipticity biases.
- For small proteins (<100 residues), random chance can yield significant geometric similarity.
Conclusions:
- The rho measure provides a universal standard for assessing protein structural similarity.
- This metric aids in evaluating NMR structure determination and protein folding models.
- Understanding rho cutoffs is crucial for accurate interpretation of protein structural comparisons.