20
|
Zhao H, Ghirlando R, Alfonso C, Arisaka F, Attali I, Bain DL, Bakhtina MM, Becker DF, Bedwell GJ, Bekdemir A, Besong TMD, Birck C, Brautigam CA, Brennerman W, Byron O, Bzowska A, Chaires JB, Chaton CT, Cölfen H, Connaghan KD, Crowley KA, Curth U, Daviter T, Dean WL, Díez AI, Ebel C, Eckert DM, Eisele LE, Eisenstein E, England P, Escalante C, Fagan JA, Fairman R, Finn RM, Fischle W, de la Torre JG, Gor J, Gustafsson H, Hall D, Harding SE, Cifre JGH, Herr AB, Howell EE, Isaac RS, Jao SC, Jose D, Kim SJ, Kokona B, Kornblatt JA, Kosek D, Krayukhina E, Krzizike D, Kusznir EA, Kwon H, Larson A, Laue TM, Le Roy A, Leech AP, Lilie H, Luger K, Luque-Ortega JR, Ma J, May CA, Maynard EL, Modrak-Wojcik A, Mok YF, Mücke N, Nagel-Steger L, Narlikar GJ, Noda M, Nourse A, Obsil T, Park CK, Park JK, Pawelek PD, Perdue EE, Perkins SJ, Perugini MA, Peterson CL, Peverelli MG, Piszczek G, Prag G, Prevelige PE, Raynal BDE, Rezabkova L, Richter K, Ringel AE, Rosenberg R, Rowe AJ, Rufer AC, Scott DJ, Seravalli JG, Solovyova AS, Song R, Staunton D, Stoddard C, Stott K, Strauss HM, Streicher WW, Sumida JP, Swygert SG, Szczepanowski RH, Tessmer I, Toth RT, Tripathy A, Uchiyama S, Uebel SFW, Unzai S, Gruber AV, von Hippel PH, Wandrey C, Wang SH, Weitzel SE, Wielgus-Kutrowska B, Wolberger C, Wolff M, Wright E, Wu YS, Wubben JM, Schuck P. A multilaboratory comparison of calibration accuracy and the performance of external references in analytical ultracentrifugation. PLoS One 2015; 10:e0126420. [PMID: 25997164 PMCID: PMC4440767 DOI: 10.1371/journal.pone.0126420] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 04/02/2015] [Indexed: 12/21/2022] Open
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.
Collapse
Affiliation(s)
- Huaying Zhao
- 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
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Carlos Alfonso
- Analytical Ultracentrifugacion and Light Scattering Facility, Centro de Investigaciones Biológicas, CSIC, Madrid, 28040, Spain
| | - Fumio Arisaka
- Life Science Research Center, Nihon University, College of Bioresource Science, Fujisawa, 252–0880, Japan
| | - Ilan Attali
- Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - David L. Bain
- Department of Pharmaceutical Sciences, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, 80045, United States of America
| | - Marina M. Bakhtina
- 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
| | - Donald F. Becker
- Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States of America
| | - Gregory J. Bedwell
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, 35294, United States of America
| | - Ahmet Bekdemir
- Supramolecular Nanomaterials and Interfaces Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland
| | - Tabot M. D. Besong
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, School of Biosciences, Sutton Bonington, LE12 5RD, United Kingdom
| | | | - Chad A. Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390, United States of America
| | - William Brennerman
- Beckman Coulter, Inc., Life Science Division, Indianapolis, Indiana, 46268, United States of America
| | - Olwyn Byron
- School of Life Sciences, University of Glasgow, Glasgow, G37TT, United Kingdom
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, 02–089, Poland
| | - Jonathan B. Chaires
- JG Brown Cancer Center, University of Louisville, Louisville, Kentucky, 40202, United States of America
| | - Catherine T. Chaton
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45267, United States of America
| | - Helmut Cölfen
- Physical Chemistry, University of Konstanz, 78457, Konstanz, Germany
| | - Keith D. Connaghan
- Department of Pharmaceutical Sciences, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, 80045, United States of America
| | - Kimberly A. Crowley
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, 01605, United States of America
| | - Ute Curth
- Institute for Biophysical Chemistry, Hannover Medical School, 30625, Hannover, Germany
| | - Tina Daviter
- Institute of Structural and Molecular Biology Biophysics Centre, Birkbeck, University of London and University College London, London, WC1E 7HX, United Kingdom
| | - William L. Dean
- JG Brown Cancer Center, University of Louisville, Louisville, Kentucky, 40202, United States of America
| | - Ana I. Díez
- Department of Physical Chemistry, University of Murcia, Murcia, 30071, Spain
| | - Christine Ebel
- Univ. Grenoble Alpes, IBS, F-38044, Grenoble, France
- CNRS, IBS, F-38044, Grenoble, France
- CEA, IBS, F-38044, Grenoble, France
| | - Debra M. Eckert
- Protein Interactions Core, Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, 84112, United States of America
| | - Leslie E. Eisele
- Wadsworth Center, New York State Department of Health, Albany, New York, 12208, United States of America
| | - Edward Eisenstein
- Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, Rockville, Maryland, 20850, United States of America
| | - Patrick England
- Institut Pasteur, Centre of Biophysics of Macromolecules and Their Interactions, Paris, 75724, France
| | - Carlos Escalante
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, 23220, United States of America
| | - Jeffrey A. Fagan
- Materials Science and Engineering Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, 20899, United States of America
| | - Robert Fairman
- Department of Biology, Haverford College, Haverford, Pennsylvania, 19041, United States of America
| | - Ron M. Finn
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | | | - Jayesh Gor
- Department of Structural and Molecular Biology, Darwin Building, University College London, London, WC1E 6BT, United Kingdom
| | | | - Damien Hall
- Research School of Chemistry, Section on Biological Chemistry, The Australian National University, Acton, ACT 0200, Australia
| | - Stephen E. Harding
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, School of Biosciences, Sutton Bonington, LE12 5RD, United Kingdom
| | | | - Andrew B. Herr
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45267, United States of America
| | - Elizabeth E. Howell
- Biochemistry, Cell and Molecular Biology Department, University of Tennessee, Knoxville, Tennessee, 37996–0840, United States of America
| | - Richard S. Isaac
- 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
| | - Shu-Chuan Jao
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
- Biophysics Core Facility, Scientific Instrument Center, Academia Sinica, Taipei, 115, Taiwan
| | - Davis Jose
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, 97403, United States of America
| | - Soon-Jong Kim
- Department of Chemistry, Mokpo National University, Muan, 534–729, Korea
| | - Bashkim Kokona
- Department of Biology, Haverford College, Haverford, Pennsylvania, 19041, United States of America
| | - Jack A. Kornblatt
- Enzyme Research Group, Concordia University, Montreal, Quebec, H4B 1R6, Canada
| | - Dalibor Kosek
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Prague, 12843, Czech Republic
| | - Elena Krayukhina
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, 565–0871, Japan
| | - Daniel Krzizike
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, United States of America
| | - Eric A. Kusznir
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-LaRoche Ltd., Basel, 4070, Switzerland
| | - Hyewon Kwon
- Analytical Biopharmacy Core, University of Washington, Seattle, Washington, 98195, United States of America
| | - Adam Larson
- 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
| | - Thomas M. Laue
- Department of Biochemistry, University of New Hampshire, Durham, New Hampshire, 03824, United States of America
| | - Aline Le Roy
- Univ. Grenoble Alpes, IBS, F-38044, Grenoble, France
- CNRS, IBS, F-38044, Grenoble, France
- CEA, IBS, F-38044, Grenoble, France
| | - Andrew P. Leech
- Technology Facility, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Hauke Lilie
- Institute of Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, 06120, Halle, Germany
| | - Karolin Luger
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, United States of America
| | - Juan R. Luque-Ortega
- Analytical Ultracentrifugacion and Light Scattering Facility, Centro de Investigaciones Biológicas, CSIC, Madrid, 28040, Spain
| | - Jia Ma
- 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
| | - Carrie A. May
- Department of Biochemistry, University of New Hampshire, Durham, New Hampshire, 03824, United States of America
| | - Ernest L. Maynard
- Department of Biochemistry, Uniformed Services University of the Health Sciences, Bethesda, Maryland, 20814, United States of America
| | - Anna Modrak-Wojcik
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, 02–089, Poland
| | - Yee-Foong Mok
- Department of Biochemistry and Molecular Biology, Bio21 Instute of Molecular Science and Biotechnology, University of Melbourne, Parkville, 3010, Victoria, Australia
| | - Norbert Mücke
- Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, 69120, Germany
| | | | - Geeta J. Narlikar
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, 94158, United States of America
| | - Masanori Noda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, 565–0871, Japan
| | - Amanda Nourse
- Molecular Interaction Analysis Shared Resource, St. Jude Children’s Research Hospital, Memphis, Tennessee, 38105, United States of America
| | - Tomas Obsil
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Prague, 12843, Czech Republic
| | - Chad K. Park
- Analytical Biophysics & Materials Characterization, Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, 85721, United States of America
| | - Jin-Ku Park
- Central Instrument Center, Mokpo National University, Muan, 534–729, Korea
| | - Peter D. Pawelek
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, H4B 1R6, Canada
| | - Erby E. Perdue
- Beckman Coulter, Inc., Life Science Division, Indianapolis, Indiana, 46268, United States of America
| | - Stephen J. Perkins
- Department of Structural and Molecular Biology, Darwin Building, University College London, London, WC1E 6BT, United Kingdom
| | - Matthew A. Perugini
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Craig L. Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, 01605, United States of America
| | - Martin G. Peverelli
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Grzegorz Piszczek
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Gali Prag
- Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Peter E. Prevelige
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, 35294, United States of America
| | - Bertrand D. E. Raynal
- Institut Pasteur, Centre of Biophysics of Macromolecules and Their Interactions, Paris, 75724, France
| | - Lenka Rezabkova
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland
| | - Klaus Richter
- Department of Chemistry and Center for Integrated Protein Science, Technische Universität München, 85748, Garching, Germany
| | - Alison E. Ringel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, United States of America
| | - Rose Rosenberg
- Physical Chemistry, University of Konstanz, 78457, Konstanz, Germany
| | - Arthur J. Rowe
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, School of Biosciences, Sutton Bonington, LE12 5RD, United Kingdom
| | - Arne C. Rufer
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-LaRoche Ltd., Basel, 4070, Switzerland
| | - David J. Scott
- Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, OX11 0FA, United Kingdom
| | - Javier G. Seravalli
- Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States of America
| | - Alexandra S. Solovyova
- Proteome and Protein Analysis, University of Newcastle, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Renjie Song
- Wadsworth Center, New York State Department of Health, Albany, New York, 12208, United States of America
| | - David Staunton
- Molecular Biophysics Suite, Department of Biochemistry, Oxford, Oxon, OX1 3QU, United Kingdom
| | - Caitlin Stoddard
- 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
| | - Katherine Stott
- Biochemistry Department, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | | | - Werner W. Streicher
- Protein Function and Interactions, Novo Nordisk Foundation Center for Protein Research, Copenhagen, 2200, Denmark
| | - John P. Sumida
- Analytical Biopharmacy Core, University of Washington, Seattle, Washington, 98195, United States of America
| | - Sarah G. Swygert
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, 01605, United States of America
| | - Roman H. Szczepanowski
- Core Facility, International Institute of Molecular and Cell Biology, Warsaw, 02–109, Poland
| | - Ingrid Tessmer
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080, Würzburg, Germany
| | - Ronald T. Toth
- Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas, 66047, United States of America
| | - Ashutosh Tripathy
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, United States of America
| | - Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, 565–0871, Japan
| | - Stephan F. W. Uebel
- Biochemistry Core Facility, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Satoru Unzai
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230–0045, Japan
| | - Anna Vitlin Gruber
- Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Peter H. von Hippel
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, 97403, United States of America
| | - Christine Wandrey
- Laboratoire de Médecine Régénérative et de Pharmacobiologie, Ecole Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland
| | - Szu-Huan Wang
- Biophysics Core Facility, Scientific Instrument Center, Academia Sinica, Taipei, 115, Taiwan
| | - Steven E. Weitzel
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, 97403, United States of America
| | - Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, 02–089, Poland
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, United States of America
| | - Martin Wolff
- ICS-6, Structural Biochemistry, Research Center Juelich, 52428, Juelich, Germany
| | - Edward Wright
- Biochemistry, Cell and Molecular Biology Department, University of Tennessee, Knoxville, Tennessee, 37996–0840, United States of America
| | - Yu-Sung Wu
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, Delaware, 19716, United States of America
| | - Jacinta M. Wubben
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Peter Schuck
- 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
- * E-mail:
| |
Collapse
|