Use of molecular mechanics for secondary structure prediction. Is it possible to reveal alpha-helix?
A new approach to predicting protein standard conformations is suggested. The idea consists in modeling by molecular mechanics tools a continuous alpha-helical conformation for the whole protein. The profile of energy along the model alpha-helix reveals minima corresponding to real alpha-helical segments in the native protein. The 3/10-helices and beta-turns including a local alpha-helical conformation may be detected as well. All alpha-helical segments in the test sample are delineated; mean residue by residue accuracy Q(3alpha) is 79%. This non-statistical approach can shed light on the physical grounds of alpha-helix formation.
Kilosanidze
Gelena T
GT
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.
Kutsenko
Alexey S
AS
Esipova
Natalia G
NG
Tumanyan
Vladimir G
VG
D002352:Carrier Proteins / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry; D004735:Energy Transfer; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012097:Repressor Proteins / Q000737:chemistry; D014764:Viral Proteins / Q000737:chemistry; D054334:Viral Regulatory and Accessory Proteins
D002352:Carrier Proteins; D004268:DNA-Binding Proteins; D011506:Proteins; D012097:Repressor Proteins; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins