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WO2000072004A3 - Method of determining the three-dimensional shape of a macromolecule - Google Patents

Method of determining the three-dimensional shape of a 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
Other languages
French (fr)
Other versions
WO2000072004A9 (en
WO2000072004A2 (en
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 JP2000620343A priority Critical patent/JP2003528288A/en
Priority to AU52989/00A priority patent/AU5298900A/en
Priority to EP00937870A priority patent/EP1277050A2/en
Publication of WO2000072004A2 publication Critical patent/WO2000072004A2/en
Publication of WO2000072004A9 publication Critical patent/WO2000072004A9/en
Publication of WO2000072004A3 publication Critical patent/WO2000072004A3/en

Links

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

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Molecular Biology (AREA)
  • Physics & Mathematics (AREA)
  • Chemical & Material Sciences (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Hematology (AREA)
  • Urology & Nephrology (AREA)
  • Biomedical Technology (AREA)
  • Immunology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biotechnology (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Medicinal Chemistry (AREA)
  • Pathology (AREA)
  • General Physics & Mathematics (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • Food Science & Technology (AREA)
  • Cell Biology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Evolutionary Biology (AREA)
  • Medical Informatics (AREA)
  • Theoretical Computer Science (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

The present invention provides a fast and efficient method for determining the three-dimensional conformation of a protein. The steps of the method of the invention include: 1) formation of physical distance constraints, e.g., forming intramolecular chemical crosslinks of known size between residues of a protein; 2) enriching the number of the molecules that have intramolecular chemical crosslinks in the reaction pool, e.g., using size separation to remove proteins with intermolecular bonds; 3) exposing the enriched reaction pool to a protease that cuts the protein at specific sites to produce peptide fragments; 4) measuring the size of the peptide fragments to determine linkage sites with a certain spatial relationship in the protein; and 5) interpreting the data produced to determine spatial geometry and protein structure based on the deduced spatial relationship of the linkage sites. The information is preferably analyzed with aid from a computer system, which can be used to generate and/or analyze distance constraints between amino acids.
PCT/US2000/014667 1999-05-26 2000-05-26 Method of determining the three-dimensional shape of a macromolecule WO2000072004A2 (en)

Priority Applications (3)

Application Number Priority Date Filing Date Title
JP2000620343A JP2003528288A (en) 1999-05-26 2000-05-26 Method for determining three-dimensional shape of polymer
AU52989/00A AU5298900A (en) 1999-05-26 2000-05-26 Method of determining the three-dimensional shape of a macromolecule
EP00937870A EP1277050A2 (en) 1999-05-26 2000-05-26 Method of determining the three-dimensional shape of a macromolecule

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 (en) 2000-11-30
WO2000072004A9 WO2000072004A9 (en) 2002-08-29
WO2000072004A3 true WO2000072004A3 (en) 2002-11-28

Family

ID=22470229

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2000/014667 WO2000072004A2 (en) 1999-05-26 2000-05-26 Method of determining the three-dimensional shape of a macromolecule

Country Status (4)

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

Families Citing this family (17)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
ITRM20010088A1 (en) 2001-02-21 2002-08-21 Idi Irccs PEPTIDE ABLE TO INHIBIT THE ACTIVITY OF THE GROWTH FACTOR DERIVED FROM THE PLATES (PDGF-BB) AND OF THE GROWTH FACTOR DERIVED FROM THE FI
JP4055772B2 (en) * 2002-04-26 2008-03-05 味の素株式会社 Protein structure analysis method, protein structure analysis apparatus, program, and recording medium
JP3743717B2 (en) 2002-06-25 2006-02-08 株式会社日立製作所 Mass spectrometry data analysis method, mass spectrometry data analysis apparatus, mass spectrometry data analysis program, and solution providing system
JP2006282929A (en) * 2005-04-04 2006-10-19 Taiyo Nippon Sanso Corp Molecular structure prediction method
ATE515697T1 (en) * 2005-05-04 2011-07-15 Eidgenoess Tech Hochschule MASS SPECTROMETRIC ANALYSIS METHOD
WO2008074769A1 (en) * 2006-12-18 2008-06-26 Covalx Ag Direct mass spectrometric analysis of aggregates of therapeutic proteins
WO2008101121A2 (en) 2007-02-14 2008-08-21 Dana-Farber Cancer Institute, Inc. Methods and compositions relating to promoter regulation by muc1 and klf proteins
US8097427B2 (en) * 2007-03-16 2012-01-17 Covalx Ag Direct mass spectrometric analysis of drug candidates targeting protein complexes
AU2009305550B2 (en) 2008-10-17 2014-06-12 Dana-Farber Cancer Institute, Inc. MUC-1 cytoplasmic domain peptides as inhibitors of cancer
JP2011152094A (en) * 2010-01-28 2011-08-11 Sony Corp Method for designing heat-resistant tyrosine-dependent oxidation-reduction enzyme and heat-resistant tyrosine-dependent oxidation-reduction enzyme
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 (en) * 2013-11-13 2015-05-21 Heider Elizabeth M Nmr crystallography methods for three-dimensional structure determination
GB201511508D0 (en) * 2015-07-01 2015-08-12 Ge Healthcare Bio Sciences Ab Method for determining a size of biomolecules
CN107449483B (en) * 2017-08-04 2019-12-06 赵德省 substance residual quantity reminding system and method
CN108469495B (en) * 2018-05-08 2020-02-07 中国海洋大学 Method for detecting fish parvalbumin by using liquid chromatography tandem mass spectrometry
CN111755065B (en) * 2020-06-15 2024-05-17 重庆邮电大学 Protein conformation prediction acceleration method based on virtual network mapping and cloud parallel computing

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

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