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WO2000072004A3 - Procede de determination de la forme tridimensionnelle d'une macromolecule - Google Patents

Procede de determination de la forme tridimensionnelle d'une macromolecule Download PDF

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Publication number
WO2000072004A3
WO2000072004A3 PCT/US2000/014667 US0014667W WO0072004A3 WO 2000072004 A3 WO2000072004 A3 WO 2000072004A3 US 0014667 W US0014667 W US 0014667W WO 0072004 A3 WO0072004 A3 WO 0072004A3
Authority
WO
WIPO (PCT)
Prior art keywords
protein
size
determining
peptide fragments
spatial relationship
Prior art date
Application number
PCT/US2000/014667
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English (en)
Other versions
WO2000072004A9 (fr
WO2000072004A2 (fr
Inventor
Bradford W Gibson
Irwin D Kuntz
Ning Tang
Gavin Dollinger
Connie M Oshiro
Judith C Hempel
Eric Taylor
Original Assignee
Univ California
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Univ California filed Critical Univ California
Priority to AU52989/00A priority Critical patent/AU5298900A/en
Priority to EP00937870A priority patent/EP1277050A2/fr
Priority to JP2000620343A priority patent/JP2003528288A/ja
Publication of WO2000072004A2 publication Critical patent/WO2000072004A2/fr
Publication of WO2000072004A9 publication Critical patent/WO2000072004A9/fr
Publication of WO2000072004A3 publication Critical patent/WO2000072004A3/fr

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Classifications

    • G—PHYSICS
    • G01—MEASURING; TESTING
    • 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
    • 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
    • G01N33/6848—Methods of protein analysis involving mass spectrometry
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B15/00—ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
    • G16B15/20—Protein or domain folding
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • 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
    • 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
    • G01N33/6818—Sequencing of polypeptides
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • 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
    • 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
    • G01N33/6842—Proteomic analysis of subsets of protein mixtures with reduced complexity, e.g. membrane proteins, phosphoproteins, organelle proteins
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • 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
    • 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
    • G01N33/6848—Methods of protein analysis involving mass spectrometry
    • G01N33/6851—Methods of protein analysis involving laser desorption ionisation mass spectrometry
    • H—ELECTRICITY
    • H01—ELECTRIC ELEMENTS
    • H01J—ELECTRIC DISCHARGE TUBES OR DISCHARGE LAMPS
    • H01J49/00—Particle spectrometers or separator tubes
    • H01J49/02—Details
    • H01J49/04—Arrangements for introducing or extracting samples to be analysed, e.g. vacuum locks; Arrangements for external adjustment of electron- or ion-optical components
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B15/00—ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment

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  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Molecular Biology (AREA)
  • Chemical & Material Sciences (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Immunology (AREA)
  • Hematology (AREA)
  • Biomedical Technology (AREA)
  • Urology & Nephrology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biotechnology (AREA)
  • Analytical Chemistry (AREA)
  • Food Science & Technology (AREA)
  • Medicinal Chemistry (AREA)
  • Cell Biology (AREA)
  • Pathology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Microbiology (AREA)
  • General Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • Theoretical Computer Science (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Evolutionary Biology (AREA)
  • Medical Informatics (AREA)
  • Optics & Photonics (AREA)
  • Other Investigation Or Analysis Of Materials By Electrical Means (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

La présente invention concerne un procédé rapide et efficace qui permet de déterminer la conformation tridimensionnelle d'une protéine. Le procédé selon l'invention comprend les étapes suivantes: 1) on établit des limites de distance physique, par exemple en formant des réticulations chimiques intramoléculaires d'une taille connue entre des restes d'une protéine; 2) on enrichit le nombre de molécules ayant des réticulations chimiques intramoléculaires dans le groupe de réaction, par exemple au moyen d'une séparation fondée sur la taille pour éliminer les protéines ayant des liaisons intermoléculaires; 3) on expose le groupe de réaction enrichi à une protéase qui coupe la protéine au niveau de sites spécifiques pour produire des fragments peptidiques; 4) on mesure la taille des fragments peptidiques pour déterminer les sites de liaison ayant une certaine relation spatiale dans la protéine; et 5) on interprète les données produites pour déterminer le géométrie spatiale et la structure de la protéine sur la base de la relation spatiale déduite des sites de liaison. Ces information sont de préférence analysées à l'aide d'un système informatique, qui peut être utilisé pour générer et/ou analyser des limites de distance entre des acides aminés.
PCT/US2000/014667 1999-05-26 2000-05-26 Procede de determination de la forme tridimensionnelle d'une macromolecule WO2000072004A2 (fr)

Priority Applications (3)

Application Number Priority Date Filing Date Title
AU52989/00A AU5298900A (en) 1999-05-26 2000-05-26 Method of determining the three-dimensional shape of a macromolecule
EP00937870A EP1277050A2 (fr) 1999-05-26 2000-05-26 Procede de determination de la forme tridimensionnelle d'une macromolecule
JP2000620343A JP2003528288A (ja) 1999-05-26 2000-05-26 高分子の三次元形状の決定方法

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US13589199P 1999-05-26 1999-05-26
US60/135,891 1999-05-26

Publications (3)

Publication Number Publication Date
WO2000072004A2 WO2000072004A2 (fr) 2000-11-30
WO2000072004A9 WO2000072004A9 (fr) 2002-08-29
WO2000072004A3 true WO2000072004A3 (fr) 2002-11-28

Family

ID=22470229

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2000/014667 WO2000072004A2 (fr) 1999-05-26 2000-05-26 Procede de determination de la forme tridimensionnelle d'une macromolecule

Country Status (4)

Country Link
EP (1) EP1277050A2 (fr)
JP (1) JP2003528288A (fr)
AU (1) AU5298900A (fr)
WO (1) WO2000072004A2 (fr)

Families Citing this family (17)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
ITRM20010088A1 (it) * 2001-02-21 2002-08-21 Idi Irccs Peptide in grado di inibire l'attivita' del fattore di crescita derivato dalle piastrine (pdgf-bb) e del fattore di crescita derivato dai fi
JP4055772B2 (ja) * 2002-04-26 2008-03-05 味の素株式会社 タンパク質構造解析方法、タンパク質構造解析装置、プログラム、および、記録媒体
JP3743717B2 (ja) * 2002-06-25 2006-02-08 株式会社日立製作所 質量分析データの解析方法および質量分析データの解析装置および質量分析データの解析プログラムならびにソリューション提供システム
JP2006282929A (ja) * 2005-04-04 2006-10-19 Taiyo Nippon Sanso Corp 分子構造予測方法
ATE515697T1 (de) * 2005-05-04 2011-07-15 Eidgenoess Tech Hochschule Massenspektrometrisches analyseverfahren
JP5302212B2 (ja) * 2006-12-18 2013-10-02 コヴァルクス・アーゲー 治療タンパク質の凝集体の直接質量分光分析
US8012695B2 (en) 2007-02-14 2011-09-06 Dana-Farber Cancer Institute, Inc. Methods and compositions relating to promoter regulation by MUC1 and KLF proteins
EP2126584B1 (fr) * 2007-03-16 2012-12-19 CovalX AG Analyse par spectrométrie de masse directe de médicaments candidats ciblant des complexes protéiques
JP5657549B2 (ja) 2008-10-17 2015-01-21 デイナ ファーバー キャンサー インスティチュート，インコーポレイテッド 癌の阻害剤としてのｍｕｃ−１細胞質ドメインペプチド
JP2011152094A (ja) * 2010-01-28 2011-08-11 Sony Corp 耐熱化チロシン依存性酸化還元酵素の設計方法及び耐熱化チロシン依存性酸化還元酵素
US9170221B2 (en) 2010-10-01 2015-10-27 Elizabeth M. HEIDER NMR crystallography methods for three-dimensional structure determination
US9194953B2 (en) * 2010-10-21 2015-11-24 Sony Corporation 3D time-of-light camera and method
WO2015072982A1 (fr) * 2013-11-13 2015-05-21 Heider Elizabeth M Procédés de cristallographie rmn pour la détermination d'une structure tridimensionnelle
GB201511508D0 (en) * 2015-07-01 2015-08-12 Ge Healthcare Bio Sciences Ab Method for determining a size of biomolecules
CN107449483B (zh) * 2017-08-04 2019-12-06 赵德省 一种物质余量的提醒系统及方法
CN108469495B (zh) * 2018-05-08 2020-02-07 中国海洋大学 一种利用液相色谱串联质谱检测鱼类小清蛋白的方法
CN111755065B (zh) * 2020-06-15 2024-05-17 重庆邮电大学 一种基于虚拟网络映射和云并行计算的蛋白质构象预测加速方法

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
FISCHER D ET AL: "PROTEIN FOLD RECOGNITION USING SEQUENCE-DERIVED PREDICTIONS", PROTEIN SCIENCE, CAMBRIDGE UNIVERSITY PRESS, CAMBRIDGE, GB, vol. 5, 1996, pages 947 - 955, XP002906968, ISSN: 0961-8368 *
NGUYEN D N ET AL: "Protein mass spectrometry: applications to analytical biotechnology", JOURNAL OF CHROMATOGRAPHY A, ELSEVIER SCIENCE, NL, vol. 705, no. 1, 23 June 1995 (1995-06-23), pages 21 - 45, XP004038936, ISSN: 0021-9673 *

Also Published As

Publication number Publication date
JP2003528288A (ja) 2003-09-24
WO2000072004A9 (fr) 2002-08-29
EP1277050A2 (fr) 2003-01-22
AU5298900A (en) 2000-12-12
WO2000072004A2 (fr) 2000-11-30

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