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Variation of folded polypeptide surface area with probe size
Author(s) -
Islam Suhail A.,
Weaver David L.
Publication year - 1991
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.340100404
Subject(s) - myoglobin , globin , helix (gastropod) , chemistry , radius , crystallography , fractal dimension , hemeprotein , alpha helix , surface (topology) , biophysics , fractal , chemical physics , heme , geometry , circular dichroism , hemoglobin , biology , biochemistry , ecology , mathematical analysis , computer security , mathematics , snail , computer science , enzyme
Three types of polypeptide surface area (contact, accessible, and molecular) have been studied as a function of the radius of a probe sphere used to map the surface. The surfaces are: (1) three α‐helices, the H‐helix of myoglobin, the E‐helix of leghemoglobin, and an artificial polyalanine helix, each with 26 residues; (2) two globins, myoglobin and leghemoglobin, each with 153 residues: and (3) a two center model system for which the three types of surface area have been calculated analytically. The two globin helices have almost identical surface areas as a function of probe size as do the two globins. The polyalanine helix surface area is smaller but similar in shape to the globin helix areas. All three helix contact areas tend to the same limit as the probe size increases, and the globin contact areas behave similarly. Fractal dimensions were calculated for the helix and globin contact and molecular surfaces. All fractal dimensions showed strong dependence on probe size. The contact fractal dimension peaks at larger values for both the helices and globins. Most residues do not make contact with large probes (15 Å).