2006 Fiscal Year Final Research Report Summary
The prediction of Solenoid Structures in Proteins by a New Helix Fitting Method
| Project/Area Number |
16310135
|
|---|
| Research Category |
Grant-in-Aid for Scientific Research (B)
|
| Allocation Type | Single-year Grants |
|---|
| Section | 一般 |
|---|
| Research Field |
基礎ゲノム科学
|
|---|
| Research Institution | Sapporo Medical University |
|---|
Principal Investigator |
MATSUSHIMA Norio Sapporo Medical University, School of Health Sciences, Professor, 保健医療学部, 教授 (60137403)
|
|---|
| Project Period (FY) |
2004 – 2006
|
| Keywords | Helix Fitting / 3(10)-helix / α-helix / ω-helix / parahelix / solenoid structure |
|---|
| Research Abstract |
The problem of fitting a helix to data arises in protein structure. A helix is described by several parameters : the helix axis, the radius and the pitch. Till now, all programs proposed have predefined one of the helix parameters. We have developed the HELFIT program for fitting helices to C^α coordinates. The 3_<10>-helix is characterized by having at least two consecutive hydrogen bonds between the main-chain carbonyl oxygen of residue i and the main-chain amide hydrogen of residue i+3. There are systematic, position-specific shifts in the backbone dihedral angles. The residues per turn and radius of regular 3_<10>-helices decrease with increasing length of helix, while the helix pitch and rise per residue increase. The fraction of regular 3_<10>-helices decreases linearly with helix length. Energy minimization; show that regular helices become less stable with increasing helix length. These findings indicate that the definition of 3_<10>-helices in terms of average, uniform dihedral angles is not appropriate and that it is inherently unstable for a polypeptide to form an extended, regular 3w-helix. We proposed that the 3_<10>-helices observed in proteins are better referred to parahelices.
|
