ジャンル分け
chemical
DiO-DPA
GEVI
Ace-mNeon, 2015 link
- FRET-opsin
- mouse & fly in vivo
Mac-mOrange, Mac-mCitrine 2014 link
- FRET-opsin
- slice
QuasAr2-palette 2014 link
- FRET-opsin (eFRET)
- culture
ASAP1 2014 link
- Ci-VSD/P & cpGFP
- slice
-
- Ci-VSD/P and pHluorin
- fly in vivo
総説 2011.
仕組みとかに深く触れててとても良い, が, ジャンルの発展が爆速なせいで古い.
eFRET probes (QuasAr2-paletteやAce(?))の登場前だね.
電位感受性ドメイン
- QuasAr
- Ace
- Mac
- Ci-VSD/P
eFRET
eFRETは
FRETで何を検知するか
- doner/acceptor距離
- 吸収スペクトラムの変化
Traditionally, FRET is used to measure the physical distance between a donor and acceptor. However, we and others have also used FRET to measure changes in the absorption spectrum of a protein via its influence on nonradiative quenching of an attached fluorescent moiety20,21,22.
従来、FRETはドナー・アクセプター間の距離測定に用いられてきた。
しかし、我々や他のグループは、タンパク質の吸収スペクトラム変化を測定するためにFRETを用いてきた.
これは蛍光ドメインのクエンチングがスペクトラム変化に影響されることを利用している.
※筆者注: moiety - 分子の一部、モチーフ的意味合い Moiety (chemistry) - Wikipedia
Ace
Acetabularia rhodopsin
- AR1: 246 AA, 27 kDa
- AR2: 247 AA,
AR
“H+ -pumping rhodopsin from the marine alga Acetabularia”
An opsin-encoding cDNA was cloned from the marine alga Acetabularia acetabulum.
H+ -pumping rhodopsin from the marine alga Acetabularia. - PubMed - NCBI
AR complete CDS, Genbank Acetabularia acetabulum rhodopsin mRNA, complete cds - Nucleotide - NCBI
AR1
We cloned an intronless, nuclear-encoded opsin gene from an EST library of Acetabularia acetabulum. Acetabularia rhodopsin I (ARI) encodes a protein of 246 amino acids with molecular weight of 27 kDa.
We here reported cloning of a novel Acetabulariarhodopsin gene with a correct termination codon
from “Acetabularia rhodopsin I is a light-stimulated proton pump”
Acetabularia rhodopsin I is a light-stimulated proton pump. - PubMed - NCBI
AR2
AR2を見つけてきた論文.
ARII consists of 247 amino acid residues…
with a profile similar to that of ARI (or AR).The opsin-encoding gene from A. acetabulum, ARII, was cloned and found to be novel but homologous to that reported previously. ARII is a light-driven proton pump, as demonstrated by the existence of a photo-induced current through Xenopus oocytes expressing ARII.
“Crystal structure of the eukaryotic light-driven proton-pumping rhodopsin, Acetabularia rhodopsin II, from marine alga”
Crystal structure of the eukaryotic light-driven proton-pumping rhodopsin, Acetabularia rhodopsin II, from marine alga. - PubMed - NCBI
AR1もAR2も釣ってきたよ
AR1 complete CDS, Genbank Acetabularia acetabulum rhodopsin I (aopI) gene, complete cds - Nucleotide - NCBI
AR2 complete CDS, Genbank Acetabularia acetabulum rhodopsin II (aopII) gene, complete cds - Nucleotide - NCBI
Ace-mNeon
Here, we present fast GEVIs (<1-ms response) that fuse the Acetabularia acetabulum rhodopsin (Ace) (11) …
11. Tsunoda SP, et al. Biophys. J. 2006;91:1471–1479.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4904846/
引用11番. AR初クローニング2006論文
私がアラインメントしたところ、AR2を利用した模様. (アラインメント結果は下記)
簡易年表
- . AR(現在のAR1?)の発見と解析. Tsunoda, et. al.. “H+ -pumping rhodopsin from the marine alga Acetabularia”
- . AR1(ARと末端が違う)の発見と解析. Lee, et. all.. “Acetabularia rhodopsin I is a light-stimulated proton pump”
- . AR2の発見と解析. Wada, et. al.. “Crystal Structure of the Eukaryotic Light-Driven Proton-Pumping Rhodopsin, Acetabularia Rhodopsin II, from Marine Alga”
alignment AR1, AR2 and Ace-mNeon
AR2をAce-mNeonに使ってるみたい.
CLUSTAL 2.1 Multiple Sequence Alignments Sequence type explicitly set to DNA Sequence format is Pearson Sequence 1: HM070407.1_AR1_aopI__complete_cds 741 bp Sequence 2: HM070408.1_AR2_aopII__complete_cds 834 bp Sequence 3: AR_sequence_of_Ace2N-mNeon_GEVI 681 bp Start of Pairwise alignments Aligning... Sequences (1:2) Aligned. Score: 58 Sequences (1:3) Aligned. Score: 56 Sequences (2:3) Aligned. Score: 78 Guide tree file created: [clustalw.dnd] There are 2 groups Start of Multiple Alignment Aligning... Group 1: Sequences: 2 Score:10972 Group 2: Sequences: 3 Score:8967 Alignment Score 8584 CLUSTAL-Alignment file created [clustalw.aln] clustalw.aln CLUSTAL 2.1 multiple sequence alignment HM070408.1_AR2_aopII__complete ------ATGGCTGACG---TTGAGACCGAAACCGGTATGATTGCCCAATG AR_sequence_of_Ace2N-mNeon_GEV ------ATGGCTGACG---TGGAAACCGAGACCGGCATGATTGCACAGTG HM070407.1_AR1_aopI__complete_ ATGTCAAACCCTAACCCTTTCCAAACCACCTTGGGAACTGATGCTCAATG * ** ** * * *** ** * *** ** ** HM070408.1_AR2_aopII__complete GATTGTGTTCGCTATTATGGCCGCAGCAGCAATAGCGTTCGGTGTTGCTG AR_sequence_of_Ace2N-mNeon_GEV GATTGTCTTTGCTATTATGGCTGCTGCTGCTATTGCTTTTGGAGTGGCTG HM070407.1_AR1_aopI__complete_ GGTAGTTTTCGCCGTCATGGCTTTGGCTGCCATTGTTTTTTCCATCGCTG * * ** ** ** * ***** ** ** ** * ** * **** HM070408.1_AR2_aopII__complete TGCATTTCCGTCCCTCTGAACTTAAGAGTGCTTACTACATCAACATCGCA AR_sequence_of_Ace2N-mNeon_GEV TGCACTTTCGGCCTTCAGAGCTGAAGAGCGCATACTATATCAACATTGCC HM070407.1_AR1_aopI__complete_ TTTAATTCCGTCCCCTTCCTCTAAGATTGACTTACTACGTCAACATAGCC * * ** ** ** ** * * ***** ******* ** HM070408.1_AR2_aopII__complete ATCTGTACCATTGCTGCTACCGCATACTATGCTATGGCCGTTAACTACCA AR_sequence_of_Ace2N-mNeon_GEV ATCTGCACTATCGCCGCTACCGCTTACTATGCAATGGCCGTGAACTACCA HM070407.1_AR1_aopI__complete_ ATCTGCACTATTGCAGCGACCGCTTATTATGCTATGGCTGTTAACGGAGG ***** ** ** ** ** ***** ** ***** ***** ** *** HM070408.1_AR2_aopII__complete AGAT------CTTACCATGAAT---------GGGGAAAGATAGGTTGTGT AR_sequence_of_Ace2N-mNeon_GEV GGAC------CTGACAATGAAT---------GGTGAAAGGCAGGTGGTCT HM070407.1_AR1_aopI__complete_ GGACAACAAGCCCACCGCCGGTACAGGAGCGGATGAGCGTCAAGTTATAT ** * ** * * ** * * ** * * HM070408.1_AR2_aopII__complete ATGCCCGATATATTGATTGGGTTTTGACCACTCCCTTGTTATTGTTGGAC AR_sequence_of_Ace2N-mNeon_GEV ACGCAAGATATATTAACTGGGTGCTGACCACACCACTGCTCCTGCTCGAT HM070407.1_AR1_aopI__complete_ ACGCCAGATACATTGATTGGGTTTTCACCACACCCTTGCTGTTATTAGAC * ** **** *** * ***** * ***** ** ** * * * ** HM070408.1_AR2_aopII__complete TTGATCGTAATGACCAAGATGGGCGGAGTGATGATCTCTTGGGTCATCGG AR_sequence_of_Ace2N-mNeon_GEV CTCATCGTCATGACCAAGATGGGCGGAGTGATGATTTCTTGGGTCATCGG HM070407.1_AR1_aopI__complete_ CTTGTATTGCTAACCAACATGCCTGCCACCATGATCGCCTGGATCATGGG * * * * ***** *** * ***** * *** **** ** HM070408.1_AR2_aopII__complete TGCTGATATTTTCATGATTGTCTTCGGTATTTTGGGAGCTTTCGAAGACG AR_sequence_of_Ace2N-mNeon_GEV CGCAGACATTTTCATGATCGTGTTTGGTATTCTGGGCGCCTTCGAGGATG HM070407.1_AR1_aopI__complete_ AGCAGACATTGCCATGATTGCATTCGGTATCATCGGCGCATTCACCGTGG ** ** *** ****** * ** ***** * ** ** *** * * HM070408.1_AR2_aopII__complete AACACAAGTTTAAATGGGTGTACTTTATTGCCGGCTGTGTCATGCAAGCT AR_sequence_of_Ace2N-mNeon_GEV AACACAAGTTCAAATGGGTGTACTTTATCGCTGGATGTGTGATGCAGGCA HM070407.1_AR1_aopI__complete_ GAAGCTA---CAAGTGGTTCTACTTTGTTGTCGGCTGCATCATGCTTGCC * * * ** *** * ****** * * ** ** * **** ** HM070408.1_AR2_aopII__complete GTCCTAACCTACGGTATGTACAATGCTACTTGGAAAGATGACTTGAAAAA AR_sequence_of_Ace2N-mNeon_GEV GTCCTGACATACGGGATGTATAACGCCACTTGGAAAGACGATCTGAAGAA HM070407.1_AR1_aopI__complete_ GTGCTAGCCTGGGGAATGATCAACCCAATCTTCAAGGAAGAACTTCAAAA ** ** * * ** *** ** * * * ** ** ** * * ** HM070408.1_AR2_aopII__complete GAGCCCCGAGTACCATAGCAGCTATGTCTCATTGTTGGTGTTCCTATCCA AR_sequence_of_Ace2N-mNeon_GEV AAGCCCCGAGTACCATAGCTCCTATGTCAGTCTGCTCGTCTTCCTGTCAA HM070407.1_AR1_aopI__complete_ GCACAAGGAATACACCGGAGCTTACACCACCCTTTTGATTTACTTGATCG * ** *** * ** * * * * * * * HM070408.1_AR2_aopII__complete TTTTGTGGGTTTTCTACCCCGTTGTCTGGGCTTTCGGAAGCGGCTCCGGA AR_sequence_of_Ace2N-mNeon_GEV TCCTCTGGGTGTTTTATCCTGTCGTGTGGGCTTTCGGGTCTGGTAGTGGC HM070407.1_AR1_aopI__complete_ TCTTGTGGGTTATCTACCCCATCGTTTGGGGATTGGGGGCTGGCGGTCAC * * ***** * ** ** * ** **** ** ** ** HM070408.1_AR2_aopII__complete GTTTTGTCTGTCGATAATGAAGCCATCTTGATGGGAATTTTGGATGTTCT AR_sequence_of_Ace2N-mNeon_GEV GTGCTGTCCGTCGACAATGAGGCCATTCTCATGGGAATCCTGGATGTGCT HM070407.1_AR1_aopI__complete_ ATCATAGGGGTGGATGTTGAGATCATCGCGATGGGAATCTTGGACTTGTT * * ** ** *** *** ******** **** * * HM070408.1_AR2_aopII__complete TGCAAAGCCTTTGTTTGGTATGGGATGTTTAATTGCCCACGAGACTATCT AR_sequence_of_Ace2N-mNeon_GEV CGCTAAGCCACTGTTTGGAATGGGGTGCCTCATTGCCCATGAGACTATCT HM070407.1_AR1_aopI__complete_ GGCTAAGCCTCTATATGCCATCGGTGTGTTGATTACTGTGGAGGTTGTTT ** ***** * * ** ** ** * *** * *** * * * HM070408.1_AR2_aopII__complete TCAAGAAGATGGAGAGCAAGGAAACTTTGATTGAGAAGGTTGTTGCAACT AR_sequence_of_Ace2N-mNeon_GEV TCAAG--------------------------------------------- HM070407.1_AR1_aopI__complete_ ACGGAAAGTTGGGTAAGGAGGAAGCTTAGCCTTTGACTGCTTGA------ * HM070408.1_AR2_aopII__complete GCTCAAGCTATTGCTTGATTAAGACTTTGATTGAGAGTACATATTTCCAT AR_sequence_of_Ace2N-mNeon_GEV -------------------------------------------------- HM070407.1_AR1_aopI__complete_ -------------------------------------------------- HM070408.1_AR2_aopII__complete ATTATTTGTTTTTGTGTGTTCAGTTTATGACTTTCCTTCATTATTATTTT AR_sequence_of_Ace2N-mNeon_GEV -------------------------------------------------- HM070407.1_AR1_aopI__complete_ -------------------------------------------------- HM070408.1_AR2_aopII__complete GCATATAA AR_sequence_of_Ace2N-mNeon_GEV -------- HM070407.1_AR1_aopI__complete_ -------- clustalw.dnd ( HM070407.1_AR1_aopI__complete_cds:0.32151, HM070408.1_AR2_aopII__complete_cds:0.09684, AR_sequence_of_Ace2N-mNeon_GEVI:0.11461);