DK1987178T3 - Fremgangsmåde til konstruktion og screening af peptidstrukturbiblioteker - Google Patents

Fremgangsmåde til konstruktion og screening af peptidstrukturbiblioteker Download PDF

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DK1987178T3
DK1987178T3 DK07750247.4T DK07750247T DK1987178T3 DK 1987178 T3 DK1987178 T3 DK 1987178T3 DK 07750247 T DK07750247 T DK 07750247T DK 1987178 T3 DK1987178 T3 DK 1987178T3
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sequences
peptide
protein
amino acid
peptides
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Paul Michael Watt
Roland Dunbrack
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Phylogica Ltd
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
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    • C07K1/00—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
    • C07K1/04—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length on carriers
    • C07K1/047—Simultaneous synthesis of different peptide species; Peptide libraries
    • C—CHEMISTRY; METALLURGY
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/001—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof by chemical synthesis
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K7/00—Peptides having 5 to 20 amino acids in a fully defined sequence; Derivatives thereof
    • C07K7/04—Linear peptides containing only normal peptide links
    • C07K7/08—Linear peptides containing only normal peptide links having 12 to 20 amino acids
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    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
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    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
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    • C12Q1/18—Testing for antimicrobial activity of a material
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    • 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
    • G01N33/6818—Sequencing of polypeptides
    • G01N33/6824—Sequencing of polypeptides involving N-terminal degradation, e.g. Edman degradation
    • G—PHYSICS
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    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
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    • 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
    • G—PHYSICS
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    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
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    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
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    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/30—Detection of binding sites or motifs
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    • G16B35/00—ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
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    • G16B35/20—Screening of libraries
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    • C40B40/04—Libraries containing only organic compounds
    • C40B40/10—Libraries containing peptides or polypeptides, or derivatives thereof
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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.
DK07750247.4T 2006-02-20 2007-02-07 Fremgangsmåde til konstruktion og screening af peptidstrukturbiblioteker DK1987178T3 (da)

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AU2006900864A AU2006900864A0 (en) 2006-02-20 Methods of constructing and screening peptide libraries
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CA2638912A1 (en) * 2006-02-20 2007-08-30 Phylogica Limited Method of constructing and screening libraries of peptide structures
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