DK1987178T3 - Fremgangsmåde til konstruktion og screening af peptidstrukturbiblioteker - Google Patents
Fremgangsmåde til konstruktion og screening af peptidstrukturbiblioteker Download PDFInfo
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- G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins
- G01N33/6818—Sequencing of polypeptides
- G01N33/6824—Sequencing of polypeptides involving N-terminal degradation, e.g. Edman degradation
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- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
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- G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
- G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
- G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
- G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins
- G01N33/6845—Methods of identifying protein-protein interactions in protein mixtures
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Claims (12)
1. Fremgangsmåde til frembringelse af et peptidbibliotek omfattende forskelligartede proteinstrukturer, hvilken fremgangsmåde omfatter: (i) opnåelse af en flerhed af aminosyresekvenser af forskelligartede proteinstrukturer fra bioinformatikkildedata og identifikation af fragmenter af proteiner, der datamæssigt er forudset til uafhængigt at danne sekundære strukturer og/eller enheder af sekundære strukturer og/eller foldninger, når de isoleres fra de flankerende sekvenser i oprindelsesproteinet, som bestemt ifølge tre kriterier for kompakthed, ikke-polært indesluttet overfladeareal og grad af uafhængighed ifølge scoringsfunktionen:
hvor: Z, H, og I er henholdsvis et fragments kompakthed, hydrofobicitet og grad af isolering, hvor: Z er det overfladeareal af fragmentet, der er tilgængeligt for opløsningsmiddel, divideret med et minimalt overfladeareal af fragmentet, der er overfladearealet af en kugle med et volumen svarende til fragmentet; H er en fraktion af indesluttet, ikke-polært areal i det fulde ikke-polære areal; I er en fraktion af overfladearealet, som er tilgængeligt for ikke-polært opløsningsmiddel, og som oprindeligt var indesluttet i det indre af et protein men eksponeret for opløsningsmiddel efter skæring i fragmentets totale overfladeareal, der er tilgængeligt for opløsningsmiddel; avg betegner et aritmetisk gennemsnit af Z1, Η1, I1, Z2, H2 og I2, hvor 1 med hævet skrift definerer Z, Η, I beregnet efter fragmentstørrelse, og hvor 2 med hævet skrift definerer Z, Η, I beregnet som en funktion af fraktionen af fragmentstørrelsen i forhold til det fulde protein; og Dev betegner en standardafvigelse af Z1, Η1, I1, Z2, H2 og I2, hvor 1 med hævet skrift definerer Z, Η, I beregnet efter fragmentstørrelse, og hvor 2 med hævet skrift definerer Z, Η, I beregnet som en funktion af fraktionen af fragmentstørrelsen i forhold til det fulde protein; (ii) frembringelse af peptider med aminosyresekvenserne opnået i (i) og (iii) visning af peptiderne i (ii), således at peptiderne danner sekundære strukturer og/eller enheder af sekundære strukturer og/eller foldninger.
2. Fremgangsmåde ifølge krav 1, hvilken fremgangsmåde endvidere omfatter identifikation af redundante sekvenser og fjernelse eller deletering af redundante sekvenser for derved at efterlade en ikke-redundant eller normaliseret flerhed af aminosyresekvenser.
3. Fremgangsmåde ifølge krav 1 eller 2, hvilken fremgangsmåde endvidere omfatter identifikation af sekvenser, der er relateret til den opnåede flerhed af aminosyresekvenser, og tilføjelse af disse sekvenser til flerheden af aminosyresekvenser.
4. Fremgangsmåde ifølge et hvilket som helst af kravene 1 til 3, hvilken fremgangsmåde endvidere omfatter mutation af peptider, der forudses at danne en sekundær struktur eller enhed af sekundære strukturer eller en foldning eller mutation af nukleinsyrer, der koder for peptiderne.
5. Fremgangsmåde ifølge et hvilket som helst af kravene 1 til 4, hvilken fremgangsmåde endvidere omfatter udførelse af kombinationer, der er udvalgt fra: (I) (a) mutation af peptider og (b) identifikation af redundante sekvenser og fjernelse eller deletering af redundante sekvenser for derved at efterlade en ikke-redundant eller normaliseret flerhed af aminosyresekvenser; (ii) (a) identifikation af sekvenser, der er relateret til den opnåede flerhed af aminosyresekvenser, og tilføjelse af disse sekvenser til flerheden af aminosyresekvenser og (b) identifikation af redundante sekvenser og fjernelse eller deletering af redundante sekvenser for derved at efterlade en ikke-redundant eller normaliseret flerhed af aminosyresekvenser; og (iii) (a) mutation af peptider og (b) identifikation af redundante sekvenser og fjernelse eller deletering af redundante sekvenser for derved at efterlade en ikke-redundant eller normaliseret flerhed af aminosyresekvenser og (c) identifikation af sekvenser, der er relateret til den opnåede flerhed af aminosyresekvenser, og tilføjelse af disse sekvenser til flerheden af aminosyresekvenser.
6. Fremgangsmåde ifølge krav 5, hvilken fremgangsmåde omfatter gentagelser af en hvilken som helst af (i) og/eller (ii) og/eller (iii) i en hvilken som helst rækkefølge for derved at frembringe et ikke-redundant og dog yderst forskelligartet datasæt.
7. Fremgangsmåde ifølge et hvilket som helst af kravene 1 til 6, hvor peptiderne frembringes ved hjælp af syntetiske eller rekombinante midler.
8. Fremgangsmåde ifølge et hvilket som helst af kravene 1 til 7, hvor peptiderne vises som grupper på en fast overflade eller en flerhed af faste overflader eller udtrykt på overfladen af en phag eller en celle ved ribosomvisning eller ved visning in vitro eller udtrykt i en celle eller en flerhed af celler.
9. Fremgangsmåde ifølge krav 2 eller 5, hvor den ikke-redundante flerhed indbefatter relaterede strukturer, der adskiller sig ved deres evne til at foldes autonomt eller ved deres ligand-bindingsaffiniteter og/eller associerings-/dissocieringskonstanter for en ligand eller ved deres kemiske modifikationer.
10. Fremgangsmåde til fremstilling af et peptidbibliotek omfattende forskelligartede proteinstrukturer, hvilken fremgangsmåde omfatter: (i) identifikation af en flerhed af aminosyresekvenser og forskelligartede proteinstrukturer fra bioinformatikkildedata og identifikation af fragmenter af proteiner, der datamæssigt er forudset til uafhængigt at danne sekundære strukturer og/eller enheder af sekundære strukturer og/eller foldninger, når de isoleres fra de flankerende sekvenser i oprindelsesproteinet, bestemt ud fra tre kriterier for kompakthed, non-polært indesluttet overfladeareal og grad af uafhængighed ifølge scoringsfunktionen:
Z, H, og I henholdsvis er et fragments kompakthed, hydrofobicitet og grad af isolering, hvor: Z er det overfladeareal af fragmentet, der er tilgængeligt for opløsningsmiddel, divideret med et minimalt overfladeareal af fragmentet, der er overfladearealet af en kugle med et volumen svarende til fragmentet; H er en fraktion af indesluttet, ikke-polært areal i det fulde ikke-polære areal; I er en fraktion af overfladearealet, som er tilgængeligt for ikke-polært opløsningsmiddel, og som oprindeligt var indesluttet i det indre af et protein men eksponeret for opløsningsmiddel efter skæring i fragmentets totale overfladeareal, der er tilgængeligt for opløsningsmiddel; avg betegner et aritmetisk gennemsnit af Z1, Η1, I1, Z2, H2 og I2, hvor 1 med hævet skrift definerer Z, Η, I beregnet efter fragmentstørrelse, og hvor 2 med hævet skrift definerer Z, Η, I beregnet som en funktion af fraktionen af fragmentstørrelsen i forhold til det fulde protein; og Dev betegner en standardafvigelse af Z1, Η1, I1, Z2, H2 og I2, hvor 1 med hævet skrift definerer Z, Η, I beregnet efter fragmentstørrelse, og hvor 2 med hævet skrift definerer Z, Η, I beregnet som en funktion af fraktionen af fragmentstørrelsen i forhold til det fulde protein; (ii) størrelsesudvælgelse af disse sekvenser i (i) for derved at identificere et undersæt af sekvenser med den gennemsnitlige længde af en uafhængig proteinfoldning; (iii) identifikation af redundante sekvenser fra sekvenserne udvalgt i (ii) og fjernelse eller deletering af redundante sekvenser for derved at efterlade en ikke-redundant flerhed af aminosyresekvenser; (iv) frembringelse af peptider fra den ikke-redundante flerhed af aminosyresekvenser i (iii); og (v) visning af peptiderne i (iv), således at peptiderne danner sekundære strukturer og/eller enheder af sekundære strukturer og/eller foldninger.
11. Fremgangsmåde ifølge krav 10, hvilken fremgangsmåde omfatter: (i) identifikation af en flerhed af aminosyresekvenser, der er i stand til at foldes uafhængigt af andre dele af proteinerne, hvori de er indeholdt i deres native kontekster; (ii) størrelsesudvælgelse af disse sekvenser i (i) for derved at identificere et undersæt af sekvenser med den gennemsnitlige længde af en uafhængig proteinfoldning; (iii) identifikation af redundante sekvenser fra sekvenserne, der er udvalgt i (ii) , og fjernelse eller deletering af redundante sekvenser for derved at efterlade en ikke-redundant flerhed af aminosyresekvenser; (iv) frembringelse af en forskelligartet sekvenspulje ved en fremgangsmåde omfattende identifikation af sekvenser, der er relateret til den ikke-redundante flerhed af aminosyresekvenser i (iii), og tilføjelse af disse sekvenser til den ikke-redundante flerhed af aminosyresekvenser i (iii) ; (v) frembringelse af peptider fra den forskelligartede pulje af sekvenser i (iv) ; og (vi) visning af peptiderne i (v), således at peptiderne danner sekundære strukturer og/eller enheder af sekundære strukturer og/eller foldninger.
12. Screeningsfremgangsmåde omfattende: (i) udførelse af en fremgangsmåde ifølge et hvilket som helst af kravene 1 til 11 for derved at frembringe et peptidbibliotek; og (ii) screening af det således frembragte peptidbibliotek for derved at identificere et peptid.
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Application Number | Priority Date | Filing Date | Title |
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AU2006900864A AU2006900864A0 (en) | 2006-02-20 | Methods of constructing and screening peptide libraries | |
PCT/US2007/003393 WO2007097923A2 (en) | 2006-02-20 | 2007-02-07 | Method of constructing and screening libraries of peptide structures |
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DK07750247.4T DK1987178T3 (da) | 2006-02-20 | 2007-02-07 | Fremgangsmåde til konstruktion og screening af peptidstrukturbiblioteker |
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EP (1) | EP1987178B1 (da) |
JP (2) | JP5576610B2 (da) |
AU (1) | AU2007218045B2 (da) |
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US7270969B2 (en) * | 1999-05-05 | 2007-09-18 | Phylogica Limited | Methods of constructing and screening diverse expression libraries |
US9575070B2 (en) * | 2001-12-04 | 2017-02-21 | Wayne State University | Neoepitope detection of disease using protein arrays |
DK1759001T3 (da) | 2004-04-21 | 2011-08-01 | Enobia Pharma Inc | Konjugat til tilførsel til knogler og fremgangsmåde til fremstilling deraf ved at målrette proteiner til knoglen |
DK1754052T3 (da) * | 2004-06-03 | 2015-09-28 | Phylogica Ltd | Modulatorer med biokemiske egenskaber |
JP5576610B2 (ja) * | 2006-02-20 | 2014-08-20 | フィロジカ リミテッド | ペプチド構造のライブラリーの構築およびスクリーニング方法 |
CN101622347A (zh) * | 2007-01-12 | 2010-01-06 | 航道生物技术有限责任公司 | 构象约束多肽序列的组合文库 |
DE102007030904A1 (de) * | 2007-07-03 | 2009-02-05 | Pharis Biotec Gmbh | Humanes zirkulierendes antivirales Albumin-Fragment (ALB-408) und seine Verwendung |
CA2694805C (en) * | 2007-07-27 | 2014-09-09 | Immatics Biotechnologies Gmbh | Immunogenic epitopes of tumour-associated antigens |
SG2014013148A (en) | 2009-03-18 | 2014-07-30 | Oncotherapy Science Inc | Neil3 peptides and vaccines including the same |
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AU2007218045A1 (en) | 2007-08-30 |
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