Key interactions in integrin ectodomain responsible for global conformational change detected by elastic network normal-mode analysis

Matsumoto, Atsushi; Kamata, Tetsuji*; Takagi, Junichi*; Iwasaki, Kenji*; Yura, Kei

Biophysical Journal, 95(6), p.2895 - 2908, 2008/09

https://doi.org/10.1529/biophysj.108.131045

Protein is activated, but the activation mechanism and generality of the conformational change remain to be elucidated. We performed normal mode analysis of the elastic network model on integrin ectodomain in the bent form and identified key residues which were influential on molecular motions. Iterative normal mode calculations demonstrated that the specific non-bonded interactions involving the key residues work as a snap to keep integrin in the bent form. The importance of the key residues for the conformational change was further verified by mutation experiments. Conservation pattern of amino acid residues among integrin family showed that the characteristic pattern of residues seen around these key residues is found in the limited groups of integrin chains.

Neutronics Calculation of Upgreded JRR-3; Supplement:Fuel,Control Rod Reflector,etc

*; ;

JAERI-M 85-062, 121 Pages, 1985/05

JAERI-M-85-062.pdf:3.04MB

no abstracts in English

Neutronics Calculation of Upgranded JRR-3 Research Reactor(Few-Group Constants)

; ;

JAERI-M 84-159, 147 Pages, 1984/09

JAERI-M-84-159.pdf:3.44MB

no abstracts in English

Snap residues for integrin activation identified by elastic network normal mode analysis

Matsumoto, Atsushi; Kamata, Tetsuji*; Iwasaki, Kenji*; Takagi, Junichi*; Yura, Kei

no journal, , 

Integrin, a membrane protein with a huge extracellular domain, participates in cell-cell and cell-extracellular matrix interactions for metazoan. A group of integrins are known to perform a large-scale structural change when they are activated, but their mechanism and generality of the conformational change in other integrins remain to be elucidated. We performed normal mode analysis based on the elastic network models of integrin in the bent form to identify key residues dominating the molecular motions toward activation. We simulated the large conformational change of integrin from the bent to the extended forms by iterative normal mode calculations and demonstrated that specific non-bonded interactions involving the key residues work as a snap to lock integrin in the bent form. The importance of the key residues for the conformational change was verified by mutation experiments.

Superimposition of a crystal structure over EM images

Iwasaki, Kenji*; Matsumoto, Atsushi; Takagi, Junichi*

no journal, , 

Superimposition of a crystal structure over 2-D EM images

Iwasaki, Kenji*; Takagi, Junichi*; Matsumoto, Atsushi

no journal, , 

no abstracts in English

Atomic model building from low resolution electron microscopy images

Matsumoto, Atsushi; Takagi, Junichi*; Iwasaki, Kenji*

no journal, , 

2D hybrid analysis; A New approach to build 3D atomic model from 2D EM image

Matsumoto, Atsushi; Takagi, Junichi*; Iwasaki, Kenji*

no journal, ,