2006 Fiscal Year Final Research Report Summary
Underlying mechanism of bio-nano-machine investigated by massive molecular dynamics method
| Project/Area Number |
15300103
|
|---|
| Research Category |
Grant-in-Aid for Scientific Research (B)
|
| Allocation Type | Single-year Grants |
|---|
| Section | 一般 |
|---|
| Research Field |
Bioinformatics/Life informatics
|
|---|
| Research Institution | The University of Tokyo |
|---|
Principal Investigator |
KITAO Akio The University of Tokyo, Institute of Molecular and Cellular Biosciences, Associate Professor, 分子細胞生物学研究所, 助教授 (30252422)
|
|---|
| Co-Investigator(Kenkyū-buntansha) |
JOTI Yasumasa The University of Tokyo, Institute of Molecular and Cellular Biosciences, Research Associate, 分子細胞生物学研究所, 助手 (30360415)
|
|---|
| Project Period (FY) |
2003 – 2006
|
| Keywords | Massive molecular dynamics / Bio-nano-machine / bacterial flagella / Salmonella / Flagellar filament / Supercoil / Conformational transition / Torque |
|---|
| Research Abstract |
Bacterial flagellar filament is a macromolecular assembly consisting of single protein, flagellin. Bacterial swimming is controlled by the conformational transitions of this filament between left- and right-handed supercoils induced by the flagellar motor torque. We present that a massive molecular dynamics simulation was successful in constructing the atomic-level supercoil structures consistent to various experimental data and further in elucidating the detailed underlying molecular mechanisms of the polymorphic supercoiling. We have found that the following three types of interactions are keys to understanding the supercoiling mechanism. "Permanent" interactions are always maintained between subunits in the various supercoil structures. "Sliding" interactions are formed between variable hydrophilic or hydrophobic residue pairs, allowing intersubunit shear without large change in energy. The formation and breakage of "switch" interactions stabilize inter- and intrasubunit interactions, respectively. We conclude that polymorphic supercoiling is due to the energy frustration between them. The transition between supercoils is achieved by a "transform and relax" mechanism : the filament structure is geometrically transformed rapidly and then slowly relaxes to energetically meta-stable states by rearranging interactions.
|
