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PLoS One. 2015 May 21;10(5):e0126420. doi: 10.1371/journal.pone.0126420. eCollection 2015.

A multilaboratory comparison of calibration accuracy and the performance of external references in analytical ultracentrifugation.

Zhao H1, Ghirlando R2, Alfonso C3, Arisaka F4, Attali I5, Bain DL6, Bakhtina MM7, Becker DF8, Bedwell GJ9, Bekdemir A10, Besong TM11, Birck C12, Brautigam CA13, Brennerman W14, Byron O15, Bzowska A16, Chaires JB17, Chaton CT18, Cölfen H19, Connaghan KD6, Crowley KA20, Curth U21, Daviter T22, Dean WL17, Díez AI23, Ebel C24, Eckert DM25, Eisele LE26, Eisenstein E27, England P28, Escalante C29, Fagan JA30, Fairman R31, Finn RM32, Fischle W32, de la Torre JG23, Gor J33, Gustafsson H34, Hall D35, Harding SE11, Cifre JG23, Herr AB18, Howell EE36, Isaac RS37, Jao SC38, Jose D39, Kim SJ40, Kokona B31, Kornblatt JA41, Kosek D42, Krayukhina E43, Krzizike D44, Kusznir EA45, Kwon H46, Larson A37, Laue TM47, Le Roy A24, Leech AP48, Lilie H49, Luger K44, Luque-Ortega JR3, Ma J1, May CA47, Maynard EL50, Modrak-Wojcik A16, Mok YF51, Mücke N52, Nagel-Steger L53, Narlikar GJ54, Noda M43, Nourse A55, Obsil T42, Park CK56, Park JK57, Pawelek PD58, Perdue EE14, Perkins SJ33, Perugini MA59, Peterson CL20, Peverelli MG59, Piszczek G60, Prag G5, Prevelige PE9, Raynal BD28, Rezabkova L61, Richter K62, Ringel AE63, Rosenberg R19, Rowe AJ11, Rufer AC45, Scott DJ64, Seravalli JG8, Solovyova AS65, Song R26, Staunton D66, Stoddard C37, Stott K67, Strauss HM34, Streicher WW68, Sumida JP46, Swygert SG20, Szczepanowski RH69, Tessmer I70, Toth RT 4th71, Tripathy A72, Uchiyama S43, Uebel SF73, Unzai S74, Gruber AV5, von Hippel PH39, Wandrey C75, Wang SH76, Weitzel SE39, Wielgus-Kutrowska B16, Wolberger C63, Wolff M53, Wright E36, Wu YS77, Wubben JM59, Schuck P1.

Author information

1
Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, 20892, United States of America.
2
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of America.
3
Analytical Ultracentrifugacion and Light Scattering Facility, Centro de Investigaciones Biológicas, CSIC, Madrid, 28040, Spain.
4
Life Science Research Center, Nihon University, College of Bioresource Science, Fujisawa, 252-0880, Japan.
5
Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, 69978, Israel.
6
Department of Pharmaceutical Sciences, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, 80045, United States of America.
7
Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, Ohio, 43210, United States of America.
8
Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States of America.
9
Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, 35294, United States of America.
10
Supramolecular Nanomaterials and Interfaces Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland.
11
National Centre for Macromolecular Hydrodynamics, University of Nottingham, School of Biosciences, Sutton Bonington, LE12 5RD, United Kingdom.
12
Structural Biology Platform IGBMC, Illkirch, 67400, France.
13
Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390, United States of America.
14
Beckman Coulter, Inc., Life Science Division, Indianapolis, Indiana, 46268, United States of America.
15
School of Life Sciences, University of Glasgow, Glasgow, G37TT, United Kingdom.
16
Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, 02-089, Poland.
17
JG Brown Cancer Center, University of Louisville, Louisville, Kentucky, 40202, United States of America.
18
Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45267, United States of America.
19
Physical Chemistry, University of Konstanz, 78457, Konstanz, Germany.
20
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, 01605, United States of America.
21
Institute for Biophysical Chemistry, Hannover Medical School, 30625, Hannover, Germany.
22
Institute of Structural and Molecular Biology Biophysics Centre, Birkbeck, University of London and University College London, London, WC1E 7HX, United Kingdom.
23
Department of Physical Chemistry, University of Murcia, Murcia, 30071, Spain.
24
Univ. Grenoble Alpes, IBS, F-38044, Grenoble, France; CNRS, IBS, F-38044, Grenoble, France; CEA, IBS, F-38044, Grenoble, France.
25
Protein Interactions Core, Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, 84112, United States of America.
26
Wadsworth Center, New York State Department of Health, Albany, New York, 12208, United States of America.
27
Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, Rockville, Maryland, 20850, United States of America.
28
Institut Pasteur, Centre of Biophysics of Macromolecules and Their Interactions, Paris, 75724, France.
29
Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, 23220, United States of America.
30
Materials Science and Engineering Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, 20899, United States of America.
31
Department of Biology, Haverford College, Haverford, Pennsylvania, 19041, United States of America.
32
Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.
33
Department of Structural and Molecular Biology, Darwin Building, University College London, London, WC1E 6BT, United Kingdom.
34
Diabetes Biophysics, Novo Nordisk A/S, Måløv, 2760, Denmark.
35
Research School of Chemistry, Section on Biological Chemistry, The Australian National University, Acton, ACT 0200, Australia.
36
Biochemistry, Cell and Molecular Biology Department, University of Tennessee, Knoxville, Tennessee, 37996-0840, United States of America.
37
Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, 94158, United States of America; Tetrad Graduate Program, University of California San Francisco, San Francisco, California, 94158, United States of America.
38
Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan; Biophysics Core Facility, Scientific Instrument Center, Academia Sinica, Taipei, 115, Taiwan.
39
Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, 97403, United States of America.
40
Department of Chemistry, Mokpo National University, Muan, 534-729, Korea.
41
Enzyme Research Group, Concordia University, Montreal, Quebec, H4B 1R6, Canada.
42
Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Prague, 12843, Czech Republic.
43
Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan.
44
Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, United States of America.
45
Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-LaRoche Ltd., Basel, 4070, Switzerland.
46
Analytical Biopharmacy Core, University of Washington, Seattle, Washington, 98195, United States of America.
47
Department of Biochemistry, University of New Hampshire, Durham, New Hampshire, 03824, United States of America.
48
Technology Facility, Department of Biology, University of York, York, YO10 5DD, United Kingdom.
49
Institute of Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, 06120, Halle, Germany.
50
Department of Biochemistry, Uniformed Services University of the Health Sciences, Bethesda, Maryland, 20814, United States of America.
51
Department of Biochemistry and Molecular Biology, Bio21 Instute of Molecular Science and Biotechnology, University of Melbourne, Parkville, 3010, Victoria, Australia.
52
Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, 69120, Germany.
53
ICS-6, Structural Biochemistry, Research Center Juelich, 52428, Juelich, Germany.
54
Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, 94158, United States of America.
55
Molecular Interaction Analysis Shared Resource, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105, United States of America.
56
Analytical Biophysics & Materials Characterization, Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, 85721, United States of America.
57
Central Instrument Center, Mokpo National University, Muan, 534-729, Korea.
58
Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, H4B 1R6, Canada.
59
Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia.
60
Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, 20892, United States of America.
61
Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland.
62
Department of Chemistry and Center for Integrated Protein Science, Technische Universität München, 85748, Garching, Germany.
63
Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, United States of America.
64
Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, OX11 0FA, United Kingdom.
65
Proteome and Protein Analysis, University of Newcastle, Newcastle upon Tyne, NE1 7RU, United Kingdom.
66
Molecular Biophysics Suite, Department of Biochemistry, Oxford, Oxon, OX1 3QU, United Kingdom.
67
Biochemistry Department, University of Cambridge, Cambridge, CB2 1GA, United Kingdom.
68
Protein Function and Interactions, Novo Nordisk Foundation Center for Protein Research, Copenhagen, 2200, Denmark.
69
Core Facility, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland.
70
Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080, Würzburg, Germany.
71
Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas, 66047, United States of America.
72
Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, United States of America.
73
Biochemistry Core Facility, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany.
74
Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230-0045, Japan.
75
Laboratoire de Médecine Régénérative et de Pharmacobiologie, Ecole Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland.
76
Biophysics Core Facility, Scientific Instrument Center, Academia Sinica, Taipei, 115, Taiwan.
77
Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, Delaware, 19716, United States of America.

Abstract

Analytical ultracentrifugation (AUC) is a first principles based method to determine absolute sedimentation coefficients and buoyant molar masses of macromolecules and their complexes, reporting on their size and shape in free solution. The purpose of this multi-laboratory study was to establish the precision and accuracy of basic data dimensions in AUC and validate previously proposed calibration techniques. Three kits of AUC cell assemblies containing radial and temperature calibration tools and a bovine serum albumin (BSA) reference sample were shared among 67 laboratories, generating 129 comprehensive data sets. These allowed for an assessment of many parameters of instrument performance, including accuracy of the reported scan time after the start of centrifugation, the accuracy of the temperature calibration, and the accuracy of the radial magnification. The range of sedimentation coefficients obtained for BSA monomer in different instruments and using different optical systems was from 3.655 S to 4.949 S, with a mean and standard deviation of (4.304 ± 0.188) S (4.4%). After the combined application of correction factors derived from the external calibration references for elapsed time, scan velocity, temperature, and radial magnification, the range of s-values was reduced 7-fold with a mean of 4.325 S and a 6-fold reduced standard deviation of ± 0.030 S (0.7%). In addition, the large data set provided an opportunity to determine the instrument-to-instrument variation of the absolute radial positions reported in the scan files, the precision of photometric or refractometric signal magnitudes, and the precision of the calculated apparent molar mass of BSA monomer and the fraction of BSA dimers. These results highlight the necessity and effectiveness of independent calibration of basic AUC data dimensions for reliable quantitative studies.

PMID:
25997164
PMCID:
PMC4440767
DOI:
10.1371/journal.pone.0126420
[Indexed for MEDLINE]
Free PMC Article

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