school of pharmacy, kitasato university, tokyo, japan. during
TRANSCRIPT
New Human Famsbase for Circle_mutation_fams of Choline dehydrogenase, mitochondrial precursor Hideaki Umeyama, Ph.D., Professor School of Pharmacy, Kitasato University 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan phone : +81-3-5791-6330 fax : +81-3-3446-9553 e-mail:[email protected] 港区白金５－９－１ 北里大学薬学部教授 （理化学研究所客員主管研究員、東北大学未来研客員教授） 梅山秀明 http://famshelp.gsc.riken.jp/famsbase/index.html http://www.pd-fams.com/index_ja.html http://www.pharm.kitasato-u.ac.jp/bmd/files/achievement.html http://www.pharm.kitasato-u.ac.jp/bmd/ ================================================ CASP7の結果、CIECLEの詳細: HTUProteins, 69, Suppl 8, 98-107 (2007)UTH 特許出願 2006-316356現未公開 =========================＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝
T1: HTTUProteins. UTTH 2007;69 Suppl 8:98-107.T T HTTULinksUTTHT
Fams-ace: a combined method to select the best model after remodeling all server
models.
HTUTerashi GUTH, HTUTakeda-Shitaka MUTH, HTUKanou KUTH, HTUIwadate MUTH, HTUTakaya DUTH, HTUHosoi AUTH, HTUOhta KUTH, HTUUmeyama H UTH.
School of Pharmacy, Kitasato University, Tokyo, Japan.
During Critical Assessment of Protein Structure Prediction (CASP7, Pacific
Grove, CA, 2006), fams-ace was entered in the 3D coordinate prediction
category as a human expert group. The procedure can be summarized by the
following three steps. (1) All the server models were refined and rebuilt utilizing
our homology modeling method. (2) Representative structures were selected
from each server, according to a model quality evaluation, based on a 3D1D
profile score (like Verify3D). (3) The top five models were selected and
submitted in the order of the consensus-based score (like 3D-Jury).
Fams-ace is a fully automated server and does not require human intervention.
In this article, we introduce the methodology of fams-ace and discuss the
successes and failures of this approach during CASP7. In addition, we discuss
possible improvements for the next CASP. (c) 2007 Wiley-Liss, Inc.
PMID: 17894329 [PubMed - indexed for MEDLINE]
Circle_mutation_fams for Choline dehydrogenase, mitochondrial precursor ==================＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝ 貴兄のモデリングしたいタンパク質は以下のものではありませんが、参照する X 線解析のPDBのデータは同じです。ホモロジー３３％程度の参考になるターゲットを探しました。 すると、sp|Q8NE62|CHDH_HUMAN Choline dehydrogenase, mitochondrial precursor (CHD) (CDH)がぴったりでした。そこで、この Choline dehydrogenase, mitochondrial precursorをモデリングしてみました。これを見れば、貴兄のモデリングしたいものの出来具合が簡単に想像できると思います。
上記は Human FAMSBASEの結果です。 次に 1置換で自由エネルギーがどれだけ変わるかを比べるための、研究をしてみましょう。 >ref_NP_060867.1_
MWCLLRGLGRPGALARGALGQQQSLGARALASAGSESRDEYSYVVVGAGSAGCVLAGRLTEDPAERVLLL
EAGPKDVRAGSKRLSWKIHMPAALVANLCDDRYNWCYHTEVQRGLDGRVLYWPRGRVWGGSSSLNAMVYV
RGHAEDYERWQRQGARGWDYAHCLPYFRKAQGHELGASRYRGADGPLRVSRGKTNHPLHCAFLEATQQAG
YPLTEDMNGFQQEGFGWMDMTIHEGKRWSAACAYLHPALSRTNLKAEAETLVSRVLFEGTRAVGVEYVKN
GQSHRAYASKEVILSGGAINSPQLLMLSGIGNADDLKKLGIPVVCHLPGVGQNLQDHLEIYIQQACTRPI
TLHSAQKPLRKVCIGLEWLWKFTGEGATAHLETGGFIRSQPGVPHPDIQFHFLPSQVIDHGRVPTQQEAY
QVHVGPMRGTSVGWLKLRSANPQDHPVIQPNYLSTETDIEDFRLCVKLTREIFAQEALAPFRGKELQPGS
HIQSDKEIDAFVRAKADSAYHPSCTCKMGQPSDPTAVVDPQTRVLGVENLRVVDASIMPSMVSGNLNAPT
IMIAEKAADIIKGQPALWDKDVPVYKPRTLATQR
Sequence
>gi|27501456|ref|NP_060867.1| choline dehydrogenase [Homo sapiens]
>gi|21759795|gb|AAH34502.1| Choline dehydrogenase [Homo sapiens]
>gi|42558901|sp|Q8NE62|CHDH_HUMAN Choline dehydrogenase, mitochondrial
precursor (CHD) (CDH)
MWCLLRGLGRPGALARGALGQQQSLGARALASAGSESRDEYSYVVVGAGSAGCVLAGRLTEDPAERVLLL
EAGPKDVRAG
SKRLSWKIHMPAALVANLCDDRYNWCYHTEVQRGLDGRVLYWPRGRVWGGSSSLNAMVYVRGHAEDYERW
QRQGARGWDY
AHCLPYFRKAQGHELGASRYRGADGPLRVSRGKTNHPLHCAFLEATQQAGYPLTEDMNGFQQEGFGWMDM
TIHEGKRWSA
ACAYLHPALSRTNLKAEAETLVSRVLFEGTRAVGVEYVKNGQSHRAYASKEVILSGGAINSPQLLMLSGI
GNADDLKKLG
IPVVCHLPGVGQNLQDHLEIYIQQACTRPITLHSAQKPLRKVCIGLEWLWKFTGEGATAHLETGGFIRSQ
PGVPHPDIQF
HFLPSQVIDHGRVPTQQEAYQVHVGPMRGTSVGWLKLRSANPQDHPVIQPNYLSTETDIEDFRLCVKLTR
EIFAQEALAP
FRGKELQPGSHIQSDKEIDAFVRAKADSAYHPSCTCKMGQPSDPTAVVDPQTRVLGVENLRVVDASIMPS
MVSGNLNAPT
IMIAEKAADIIKGQPALWDKDVPVYKPRTLATQR
NCBI infomation
[Q8NE62]
HTUhttp://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=42558901UTH
COMMENT [CATALYTIC ACTIVITY] Choline + acceptor = betaine aldehyde +
reduced acceptor.
[COFACTOR] FAD (By similarity).
[PATHWAY] Amine and polyamine biosynthesis; betaine
biosynthesis
via choline pathway; betaine aldehyde from choline (cytochrome
c
reductase route): step 1/1.
[SUBCELLULAR LOCATION] Mitochondrion (Potential).
[SIMILARITY] Belongs to the GMC oxidoreductase family.
FEATURES Location/Qualifiers
source 1..594
/organism="Homo sapiens"
/db_xref="taxon:HTU9606UTH"
HTUgeneUTH 1..594
/gene="CHDH"
HTUProteinUTH 1..594
/gene="CHDH"
/product="Choline dehydrogenase, mitochondrial
precursor"
/EC_number="HTU1.1.99.1UTH"
ここからは、アミノ酸残基の 1置換タンパク質で、自由エネルギーが安定にな
る順番に並べたものです。
まず、簡易サークル計算で、circle 値がゼロ以上になるものについて、すべて
FAMS プログラムでモデリングを行い、自由エネルギーのスコア化である circle
値を一番大きくするものの 1置換タンパク質から順番に並べたものです。
下記の図は、貴兄が自由エネルギーの安定なタンパク質を創製することを補助
するものです。
D76W 7.6 サークルスコアだけ安定
L134M 6.7 サークルスコアだけ安定
A298S 6.6. サークルスコアだけ安定
など実験をしてみませんか。
====================================================
CASP7 の結果、CIECLEの詳細:
HTUProteins, 69, Suppl 8, 98-107 (2007)UTH
特許出願 2006-316356 現未公開
T 1: HTTUProteins. UTTH 2007;69 Suppl 8:98-107.T T HTTULinksUTTHT
Fams-ace: a combined method to select the best model after remodeling all server
models.
HTUTerashi GUTH, HTUTakeda-Shitaka MUTH, HTUKanou KUTH, HTUIwadate MUTH, HTUTakaya DUTH, HTUHosoi AUTH, HTUOhta KUTH, HTUUmeyama H UTH.
School of Pharmacy, Kitasato University, Tokyo, Japan.
During Critical Assessment of Protein Structure Prediction (CASP7, Pacific
Grove, CA, 2006), fams-ace was entered in the 3D coordinate prediction
category as a human expert group. The procedure can be summarized by the
following three steps. (1) All the server models were refined and rebuilt utilizing
our homology modeling method. (2) Representative structures were selected
from each server, according to a model quality evaluation, based on a 3D1D
profile score (like Verify3D). (3) The top five models were selected and
submitted in the order of the consensus-based score (like 3D-Jury).
Fams-ace is a fully automated server and does not require human intervention.
In this article, we introduce the methodology of fams-ace and discuss the
successes and failures of this approach during CASP7. In addition, we discuss
possible improvements for the next CASP. (c) 2007 Wiley-Liss, Inc.
PMID: 17894329 [PubMed - indexed for MEDLINE]
