Energetics of the structure and chain tilting of antiparallel beta-barrels in proteins.
The preferred structural pattern of antiparallel beta-barrels in proteins, described as the right-handed tilting of the peptide strands with respect to the axis of the barrel, is accounted for in terms of intra- and interchain interaction energies. It is related to the preference of beta-sheets for right-handed twisting. Conformational energy computations have been carried out on three eight-stranded antiparallel beta-barrels composed of six-residue strands, in which L-Val and Gly alternate, and having a right-handed, a left-handed, or no tilt. After energy minimization, the relative energies of these structures were 0.0, 8.6, and 46.1 kcal/mol, respectively; i.e., the right-tilted beta-barrel is favored energetically, in agreement with anti-parallel beta-barrels observed in proteins. Tilting of the barrel is favored, relative to the nontilted structure, by both intra- and interstrand interactions, because tilting allows better packing of the bulky side chains. On the other hand, the energy difference between the left- and right-tilted barrels arises essentially from intrachain interactions. This is a consequence of the preference of beta-sheets for a right-handed twist. Space limitations inside the barrel are satisfied if there is an alternation of bulky residues and residues with small or no side chain (preferably Gly) in neighboring positions on adjacent strands. Such a pattern is seen frequently in antiparallel beta-barrels of globular proteins. The computations indicate that a structure with Val...Gly pairs can be accommodated in a beta-barrel with no distortion.
Chou
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KC
Computational Chemistry Unit, Upjohn Company, Kalamazoo, Michigan 49001.
Heckel
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A
Némethy
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G
Rumsey
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S
Carlacci
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L
Scheraga
H A
HA
D000465:Algorithms; D000595:Amino Acid Sequence; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013237:Stereoisomerism; D013816:Thermodynamics
D011506:Proteins