SPM

SPM

SPM [Part3:]

Advanced Algorithm & Systems

2018.1.4

[Part3: ] https://www.aasri.jp/pub/spm/pdf/catalog/imagepamphlet/SPM_ApplicationField.pdf https://www.aasri.jp/pub/spm/SPM_simulator_application_examples.html

SPM

SPM

SPM SPM

SPM

GeoAFM Rhodopsin AFM (a) Cytoplasmic surface

PDB1F88 CytoplasmicExtracellular PDB3PXOCytoplasmicExtracellular

(b) Extracellular surface

GeoAFM

AFM

GeoAFM AFM

SPM

https://www.aasri.jp/pub/spm/pdf/catalog/imagepamphlet/SPM_ApplicationField.pdfhttps://www.aasri.jp/pub/spm/SPM_simulator_application_examples.html

GeoAFM(AFM) CalcImage RhodopsinAFM

GeoAFM RhodopsinCytoplasmic surface

[GeoAFM_CalcImage_Polymer_013]

https://www.aasri.jp/pub/spm/project_samples/GeoAFM/CalcImage/GeoAFM_CalcImage.php

GeoAFM AFM

TOPGeoAFM

[Show Simulated Image]

GeoAFM

AFM

Cytoplasmic surfacedisk membrane

AFM

Rhodopsin_12units_1n3m_SetModel.xyz(SetModel)PDB1N3M

https://www.aasri.jp/pub/spm/project_samples/GeoAFM/CalcImage/GeoAFM_CalcImage.php

PDB1N3MCartoon

Add SampleCartooncone( 1.0 30.0resolution = 10

PDB1N3MBallStickCartoon

PDB1N3M

PDB1N3M

Cartoon

TOP TOP

TOP

Analyzer

GeoAFMcube

GeoAFMExport Simulated Data

cube

ToolAnalyzer

AnalyzerAnalyzercube

Analyzer Analyzer

Analyzer[Rainbow] Analyzer[Rainbow] Analyzer[Rainbow] D

TOPFRONTSIDE

TOP TOP

FRONT FRONT

SIDE SIDE

2

disk membrane

G

GGPCR

2RodCone

(opsin)

11-G 11-

ohhs-ap-biology-chapter-50-presentation-74-728 Chemistry and Biology of the Initial Steps in Vision: The Friedenwald Lecture

OHHS AP Biology Chapter 50 Presentation Krzysztof Palczewski Investigative Ophthalmology & Visual Science October 2014,

Vol.55, 6651-6672. doi:10.1167/iovs.14-15502

(dimer)2 ()

3 4 Wikipedia

1F88 (PDB) 3PXO (PDB)disk membraneAFM

Cis-retinal1F88 (PDB)Trans-retinal3PXO (PDB)

Bovine Rhodopsin with Cis-retinal(Inactivated Rhodopsin)

Crystal structure of rhodopsin: A G protein-coupled receptor. Palczewski, K. ,etc Journal: (2000) Science 289: 739-745(PubMed) 1F88 (PDB)

Bovine Rhodopsin with Trans-retinal(Activated Rhodopsin)

Crystal structure of metarhodopsin II. Choe, H.W., etc, Journal: (2011) Nature 471: 651-655 (PubMed) 3PXO (PDB)

Cis-retinalInactivated

Rhodopsin 1F88 (PDB)

Trans-retinalActivated

Rhodopsin 3PXO (PDB)

PDB1F88AFM

GeoAFM_CalcImage_Polymer_1f88_Cytoplasmic GeoAFM_CalcImage_Polymer_1f88_Extracellular

1F88 (PDB) 11- AFM 33Cytoplasmic

Extracellular(SetModel)

GeoAFM(AFM)AFM

GeoAFMExport Simulated Datacube

ToolAnalyzerAnalyzerAnalyzercube

3DViewColorRainbow

CytoplasmicExtracellularCartoon

PDB1F88Cartoon

1F88 (PDB) Cytoplasmic 1F88 (PDB) Extracellular

https://www.aasri.jp/pub/spm/project_file_for_beginners_version/GeoAFM_CalcImage_Polymer_1f88_Cytoplasmic.ziphttps://www.aasri.jp/pub/spm/project_file_for_beginners_version/GeoAFM_CalcImage_Polymer_1f88_Extracellular.zip

PDB3PXOAFM

GeoAFM_CalcImage_Polymer_3pxo1_Cytoplasmic GeoAFM_CalcImage_Polymer_3pxo1_Extracellular

3PXO (PDB)

AFM 33Cytoplasmic

Extracellular(SetModel)

GeoAFM(AFM)AFM

GeoAFMExport Simulated Datacube

ToolAnalyzerAnalyzerAnalyzercube

3DViewColorRainbow

CytoplasmicExtracellularCartoon

Cartoon PDB3PXOCartoon

3PXO (PDB) Cytoplasmic 3PXO (PDB) Extracellular

https://www.aasri.jp/pub/spm/project_file_for_beginners_version/GeoAFM_CalcImage_Polymer_3pxo1_Cytoplasmic.ziphttps://www.aasri.jp/pub/spm/project_file_for_beginners_version/GeoAFM_CalcImage_Polymer_3pxo1_Extracellular.zip

(SetModel) SPMAdd Sample

EditAdd SampleFile

CartoonBallStick

AFM

GeoAFM(AFM)AFM

GeoAFM

AFM

GeoAFM

AFM

GeoAFM RhodopsinExtracellular surface

[GeoAFM_CalcImage_Polymer_013]

https://www.aasri.jp/pub/spm/project_samples/GeoAFM/CalcImage/GeoAFM_CalcImage.php

GeoAFM AFM

Analyzer[Rainbow]

GeoAFM

AFM

Extracellular surfacedisk membrane

AFM

Rhodopsin_12units_1n3m_SetModel.xyz(SetModel)PDB1N3MExtracellular surface

PDB1N3MCartoon

https://www.aasri.jp/pub/spm/project_samples/GeoAFM/CalcImage/GeoAFM_CalcImage.php

Ball

GeoAFM (AFM) CalcImage

GeoAFM AFM

[GeoAFM_CalcImage_Polymer_020]

https://www.aasri.jp/pub/spm/project_samples/GeoAFM/CalcImage/GeoAFM_CalcImage.php

GeoAFM AFM

AFM

PDB2ZW3pyramid( 25

https://www.aasri.jp/pub/spm/project_samples/GeoAFM/CalcImage/GeoAFM_CalcImage.php

Z

AFM

PDB2ZW3D

wikipedia

(Connexon) 62

2

1-2kDa(wikipedia)

Da[dalton] 12 (12C)

1/121 uunified atomic mass unit 1 Da 6

Cx26

( 26 3.5 Nature 458, 7238 | Published: 2009 4 2 | doi: 10.1038/nature07869

)

Analyzer

GradationD-ViewRainbow

GeoAFMAFM project_file_for_beginners_version_GeoAFM_CalcImage_Polymer_020

PDB2ZW3AFM

PDB2ZW3AFM

CartoonBallCartoon

2

AFM

2ZW3Cartoon2ZW3

CartoonBallBallStick

https://www.aasri.jp/pub/spm/project_file_for_beginners_version/project_file_for_beginners_version_GeoAFM_CalcImage_Polymer_020.zip

2ZW3

2ZW3

TOPAFM

Cartoon

Ball&Stick

GeoAFMExport Simulated Data

cube

ToolAnalyzer

Analyzer

Analyzercube

AnalyzerDViewRainbow

3DViewColorRainbow

AnalyzerDViewRainbow

PDB2ZW3

PDB2ZW3OPEN

CLOSE

SPM

V20170313 V20160722 1 2

GeoAFM

AFM

AFM

[GeoAFM] [Show

Simulated Sample]

Analyzer

(SPM)

()