Helix signals in proteins.
The alpha helix, first proposed by Pauling and co-workers, is a hallmark of protein structure, and much effort has been directed toward understanding which sequences can form helices. The helix hypothesis, introduced here, provides a tentative answer to this question. The hypothesis states that a necessary condition for helix formation is the presence of residues flanking the helix termini whose side chains can form hydrogen bonds with the initial four-helix greater than N-H groups and final four-helix greater than C-O groups; these eight groups would otherwise lack intrahelical partners. This simple hypothesis implies the existence of a stereochemical code in which certain sequences have the hydrogen-bonding capacity to function as helix boundaries and thereby enable the helix to form autonomously. The three-dimensional structure of a protein is a consequence of the genetic code, but the rules relating sequence to structure are still unknown. The ensuing analysis supports the idea that a stereochemical code for the alpha helix resides in its boundary residues.
Presta
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Department of Biological Chemistry, Hershey Medical Center, Pennsylvania State University, Hershey 17033.
Rose
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D000595:Amino Acid Sequence; D000818:Animals; D002268:Carboxypeptidases; D043422:Carboxypeptidases A; D003574:Cytochrome c Group; D005418:Flavodoxin; D006801:Humans; D006860:Hydrogen Bonding; D008956:Models, Chemical; D008969:Molecular Sequence Data; D009113:Muramidase; D009211:Myoglobin; D010191:Pancreatic Polypeptide; D010320:Parvalbumins; D010970:Plastocyanin; D011487:Protein Conformation; D012260:Ribonucleases; D012604:Scorpion Venoms; D013762:Tetrahydrofolate Dehydrogenase; D014305:Triose-Phosphate Isomerase; D014361:Trypsin Inhibitors; D014961:X-Ray Diffraction
D003574:Cytochrome c Group; D005418:Flavodoxin; D009211:Myoglobin; D010320:Parvalbumins; D012604:Scorpion Venoms; D014361:Trypsin Inhibitors; C009725:pancreatic polypeptide, avian; D010191:Pancreatic Polypeptide; D010970:Plastocyanin; D013762:Tetrahydrofolate Dehydrogenase; D012260:Ribonucleases; D009113:Muramidase; D002268:Carboxypeptidases; D043422:Carboxypeptidases A; D014305:Triose-Phosphate Isomerase