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1. (WO2019049663) METHOD FOR ASSESSING SUITABILITY OF ARTIFICIAL PROTEIN INCLUDING AMINO ACID RESIDUE DERIVED FROM NON-NATURALLY-OCCURRING AMINO ACID, FOR SYNTHESIS BY RIBOSOMES
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Pub. No.: WO/2019/049663 International Application No.: PCT/JP2018/030934
Publication Date: 14.03.2019 International Filing Date: 22.08.2018
IPC:
C07K 1/00 (2006.01) ,C12N 15/11 (2006.01) ,C12P 21/00 (2006.01) ,G06F 19/16 (2011.01)
C CHEMISTRY; METALLURGY
07
ORGANIC CHEMISTRY
K
PEPTIDES
1
General processes for the preparation of peptides
C CHEMISTRY; METALLURGY
12
BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
N
MICRO-ORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICRO-ORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
15
Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
09
Recombinant DNA-technology
11
DNA or RNA fragments; Modified forms thereof
C CHEMISTRY; METALLURGY
12
BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
P
FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
21
Preparation of peptides or proteins
G PHYSICS
06
COMPUTING; CALCULATING; COUNTING
F
ELECTRIC DIGITAL DATA PROCESSING
19
Digital computing or data processing equipment or methods, specially adapted for specific applications
10
Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
16
for molecular structure, e.g. structure alignment, structural or functional relations, protein folding, domain topologies, drug targeting using structure data, involving two-dimensional or three-dimensional structures
Applicants:
小俣 賢三 OMATA, Kenzo [JP/JP]; JP
Inventors:
小俣 賢三 OMATA, Kenzo; JP
Agent:
辻田 朋子 TSUJITA, Tomoko; JP
Priority Data:
2017-17335308.09.2017JP
2018-10145828.05.2018JP
Title (EN) METHOD FOR ASSESSING SUITABILITY OF ARTIFICIAL PROTEIN INCLUDING AMINO ACID RESIDUE DERIVED FROM NON-NATURALLY-OCCURRING AMINO ACID, FOR SYNTHESIS BY RIBOSOMES
(FR) PROCÉDÉ PERMETTANT D'ÉVALUER LA CONVENANCE D'UNE PROTÉINE ARTIFICIELLE COMPRENANT UN RÉSIDU D'ACIDE AMINÉ DÉRIVÉ D'UN ACIDE AMINÉ D'ORIGINE NON NATURELLE, POUR SYNTHÈSE PAR DES RIBOSOMES
(JA) 非天然アミノ酸由来のアミノ酸残基を含む人工タンパク質のリボソームによる合成への適性推測方法
Abstract:
(EN) The present invention addresses the problem of providing a method for assessing whether or not an artificial protein having a specific introduced non-naturally-occurring amino acid can be synthesized by the synthesis system provided by ribosomes. This method comprises steps a and b. (Step a): A step for performing transition state structure optimization calculation (TS optimization calculation) by a molecular orbital method or performing approximation calculation which can reproduce the transition state optimization structure, using, as an initial structure, a reaction transition state (general formula (3-1), (3-2), (3-3), (3-4), or (3-5)) in a peptidyl group transfer reaction between aminoacyl-tRNA of the non-naturally-occurring amino acid represented by general formula (1), and peptidyl-tRNA having any amino acid sequence represented by general formula (2-1) or (2-2). (Step b) A step for determining that the non-naturally-occurring amino acid has high enough suitability to be introduced into a protein in the protein synthesis system provided by ribosomes if the structure obtained as a result of step a can be assumed to be a transition state structure.
(FR) La présente invention aborde le problème consistant à fournir un procédé permettant d'évaluer l'opportunité d'une protéine artificielle ayant un acide aminé d'origine non naturelle introduit de manière spécifique à être synthétisée par le système de synthèse fourni par des ribosomes. Le procédé selon l'invention comprend les étapes a et b. (Étape a) : une étape consistant à réaliser un calcul d'optimisation d'état de transition de structure (calcul d'optimisation ET) par un procédé orbital moléculaire ou réaliser un calcul d'approximation qui peut reproduire la structure d'optimisation d'état de transition, au moyen, en tant que structure initiale, d'un état de transition de réaction (formule générale (3-1), (3-2), (3-3), (3-4), ou (3-5)) dans une réaction de transfert de groupe peptidyle entre l'aminoacyl-ARNt de l'acide aminé d'origine non naturelle représenté par la formule générale (1), et un peptidyle-ARNt ayant une séquence d'acides aminés quelconque représenté par la formule générale (2-1) ou (2-2). (Étape b) : une étape consistant à déterminer si l'acide aminé d'origine non naturelle possède un caractère approprié suffisamment élevé pour être introduit dans une protéine dans le système de synthèse de protéines fourni par des ribosomes, si la structure obtenue à la suite de l'étape a peut être supposée être une structure d'état de transition.
(JA) 本発明の解決しようとする課題は、特定の非天然アミノ酸を導入した人工タンパク質をリボソームによる合成系による合成が可能であるか否か推測する方法を提供する。 以下のa及びb工程を備える方法。 (a工程) 一般式(1)で表される前記非天然アミノ酸のアミノアシルtRNAと、 一般式(2-1)又は(2-2)で表される任意のアミノ酸配列を有するペプチジルtRNAと、 のペプチジル基転移反応における反応遷移状態(一般式(3-1)、(3-2)、(3-3)、(3-4)又は(3-5))を初期構造として、分子軌道法による遷移状態構造最適化計算(TS最適化計算)又はその遷移状態最適化構造を再現し得る近似計算を行う工程。 (b工程) 前記a工程の結果得られる構造が遷移状態構造であることが想定できる場合に、リボソームによるタンパク質合成系における、前記非天然アミノ酸のタンパク質への導入適性が高いと判断する工程。
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African Regional Intellectual Property Organization (ARIPO) (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW)
Eurasian Patent Office (AM, AZ, BY, KG, KZ, RU, TJ, TM)
European Patent Office (EPO) (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TR)
African Intellectual Property Organization (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG)
Publication Language: Japanese (JA)
Filing Language: Japanese (JA)