1
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Janke JJ, Starr CG, Kingsbury JS, Furtmann N, Roberts CJ, Calero-Rubio C. Computational Screening for mAb Colloidal Stability with Coarse-Grained, Molecular-Scale Simulations. J Phys Chem B 2024; 128:1515-1526. [PMID: 38315822 DOI: 10.1021/acs.jpcb.3c05303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Monoclonal antibodies (mAbs) are an important modality of protein therapeutics with broad applications for numerous diseases. However, colloidal instabilities occurring at high protein concentrations can limit the ability to develop stable, high-concentration liquid dosage forms that are required for patient-centric, device-mediated products. Therefore, it is advantageous to identify colloidally stable mAbs early in the discovery process to ensure that they are selected for development. Experimental screening for colloidal stability can be time- and resource-consuming and is most feasible at the later stages of drug development due to material requirements. Alternatively, computational approaches have emerging potential to provide efficient screening and focus developmental efforts on mAbs with the greatest developability potential, while providing mechanistic relationships for colloidal instability. In this work, coarse-grained, molecular-scale models were fine-tuned to screen for colloidal stability at amino-acid resolution. This model parameterization provides a framework to screen for mAb self-interactions and extrapolate to bulk solution behavior. This approach was applied to a wide array of mAbs under multiple buffer conditions, demonstrating the utility of the presented computational approach to augment early candidate screening and later formulation strategies for protein therapeutics.
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Affiliation(s)
- J Joel Janke
- Biologics Drug Product Development and Manufacturing, Sanofi, Framingham, Massachusetts 01701, United States
| | - Charles G Starr
- Biologics Drug Product Development and Manufacturing, Sanofi, Framingham, Massachusetts 01701, United States
| | - Jonathan S Kingsbury
- Biologics Drug Product Development and Manufacturing, Sanofi, Framingham, Massachusetts 01701, United States
| | - Norbert Furtmann
- Large Molecules Research Platform, Sanofi-Aventis Deutschland GmbH, Frankfurt 65926, Germany
| | - Christopher J Roberts
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Cesar Calero-Rubio
- Biologics Drug Product Development and Manufacturing, Sanofi, Framingham, Massachusetts 01701, United States
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2
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Dauer K, Kamm W, Wagner KG, Pfeiffer-Marek S. High-Throughput Screening for Colloidal Stability of Peptide Formulations Using Dynamic and Static Light Scattering. Mol Pharm 2021; 18:1939-1955. [PMID: 33789055 DOI: 10.1021/acs.molpharmaceut.0c01028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Selection of an appropriate formulation to stabilize therapeutic proteins against aggregation is one of the most challenging tasks in early-stage drug product development. The amount of aggregates is more difficult to quantify in the case of peptides due to their small molecular size. Here, we investigated the suitability of diffusion self-interaction parameters (kD) and osmotic second virial coefficients (B22) for high-throughput (HT) screening of peptide formulations regarding their aggregation risk. These parameters were compared to the effect of thermal stress on colloidal stability. The formulation matrix comprised six buffering systems at two selected pH values, four tonicity agents, and a common preservative. The results revealed that electrostatic interactions are the main driver to control colloidal stability. Preferred formulations consisted of acetate and succinate buffer at pH 4.5 combined with glycerol or mannitol and optional m-cresol. kD proved to be a suitable surrogate for B22 as an indicator of high colloidal stability in the case of peptides as was previously described for globular proteins and antibodies. Formulation assessment solely based on kD obtained by HT methods offers important insights into the optimization of colloidal stability during the early development of peptide-based liquid formulations and can be performed with a limited amount of peptide (∼360 mg).
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Affiliation(s)
- Katharina Dauer
- Department of Pharmaceutical Technology and Biopharmaceutics, Institute of Pharmacy, University of Bonn, Gerhard-Domagk-Str. 3, 53121 Bonn, Germany.,Pharmaceutical Development Platform, Tides Drug Product Pre-Development Sciences, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Walter Kamm
- Pharmaceutical Development Platform, Tides Drug Product Pre-Development Sciences, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Karl Gerhard Wagner
- Department of Pharmaceutical Technology and Biopharmaceutics, Institute of Pharmacy, University of Bonn, Gerhard-Domagk-Str. 3, 53121 Bonn, Germany
| | - Stefania Pfeiffer-Marek
- Pharmaceutical Development Platform, Tides Drug Product Pre-Development Sciences, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt am Main, Germany
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3
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Mrozowich T, Winzor DJ, Scott DJ, Patel TR. Experimental determination of second virial coefficients by small-angle X-ray scattering: a problem revisited. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:781-787. [PMID: 31667558 DOI: 10.1007/s00249-019-01404-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 10/01/2019] [Accepted: 10/10/2019] [Indexed: 11/24/2022]
Abstract
This investigation examines the validity of employing single-solute theory to interpret SAXS measurements on buffered protein solutions-the current practice despite the necessity to regard the buffer components as additional non-scattering solutes rather than as part of the solvent. The present study of bovine serum albumin in phosphate-buffered saline supplemented with 20-100 g/L sucrose as small cosolute has certainly verified the prediction that the experimentally obtained second virial coefficient should contain protein-cosolute contributions. Nevertheless, the second virial coefficient determined for protein solutions supplemented with high cosolute concentrations on the basis of single-solute theory remains a valid means for identifying conditions conducive to protein crystallization, because the return of a slightly negative second virial coefficient based on single-solute theory [Formula: see text] still establishes the existence of slightly associative interactions between protein molecules, irrespective of the molecular source-protein self-interactions and/or protein-cosolute contributions.
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Affiliation(s)
- Tyler Mrozowich
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB, T1K 3M4, Canada
| | - Donald J Winzor
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, 4072, Australia
| | - David J Scott
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK. .,ISIS Spallation Neutron and Muon Source, Rutherton Appleton Research Complex at Harwell, Harwell, OX11 OFA, UK.
| | - Trushar R Patel
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB, T1K 3M4, Canada. .,Department of Microbiology, Immunology and Infectious Disease, Cumming School of Medicine, University of Calgary, Calgary, T2N 1N4, AB, Canada. .,Li Ka Shing Institute of Virology and Discovery Lab, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
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4
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Zhang Y, Yates EV, Hong L, Saar KL, Meisl G, Dobson CM, Knowles TPJ. On-chip measurements of protein unfolding from direct observations of micron-scale diffusion. Chem Sci 2018; 9:3503-3507. [PMID: 29780480 PMCID: PMC5934698 DOI: 10.1039/c7sc04331g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 02/09/2018] [Indexed: 11/26/2022] Open
Abstract
The unfolding process of BSA in solution as a function of pH was studied by microfluidic diffusional sizing device.
Investigations of protein folding, unfolding and stability are critical for the understanding of the molecular basis of biological structure and function. We describe here a microfluidic approach to probe the unfolding of unlabelled protein molecules in microliter volumes. We achieve this objective through the use of a microfluidic platform, which allows the changes in molecular diffusivity upon folding and unfolding to be detected directly. We illustrate this approach by monitoring the unfolding of bovine serum albumin in solution as a function of pH. These results show the viability of probing protein stability on chip in small volumes.
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Affiliation(s)
- Yuewen Zhang
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK . ; ; Tel: +44 (0)1223 336344
| | - Emma V Yates
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK . ; ; Tel: +44 (0)1223 336344
| | - Liu Hong
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK . ; ; Tel: +44 (0)1223 336344.,Zhou Pei-Yuan Center for Applied Mathematics , Tsinghua University , Beijing , 10084 , P. R. China
| | - Kadi L Saar
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK . ; ; Tel: +44 (0)1223 336344
| | - Georg Meisl
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK . ; ; Tel: +44 (0)1223 336344
| | - Christopher M Dobson
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK . ; ; Tel: +44 (0)1223 336344
| | - Tuomas P J Knowles
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK . ; ; Tel: +44 (0)1223 336344.,Cavendish Laboratory , University of Cambridge , J J Thomson Avenue , Cambridge , CB3 0HE , UK
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5
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Manning MC, Liu J, Li T, Holcomb RE. Rational Design of Liquid Formulations of Proteins. THERAPEUTIC PROTEINS AND PEPTIDES 2018; 112:1-59. [DOI: 10.1016/bs.apcsb.2018.01.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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6
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Scott DJ. Accounting for thermodynamic non-ideality in the Guinier region of small-angle scattering data of proteins. Biophys Rev 2016; 8:441-444. [PMID: 28203306 PMCID: PMC5283502 DOI: 10.1007/s12551-016-0235-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 10/14/2016] [Indexed: 11/25/2022] Open
Abstract
Hydrodynamic studies of the solution properties of proteins and other biological macromolecules are often hard to interpret when the sample is present at a reasonably concentrated solution. The reason for this is that solutions exhibit deviations from ideal behaviour which is manifested as thermodynamic non-ideality. The range of concentrations at which this behaviour typically is exhibited is as low as 1–2 mg/ml, well within the range of concentrations used for their analysis by techniques such as small-angle scattering. Here we discuss thermodynamic non-ideality used previously used in the context of light scattering and sedimentation equilibrium analytical ultracentrifugation and apply it to the Guinier region of small-angle scattering data. The results show that there is a complementarity between the radially averaged structure factor derived from small-angle X-ray scattering/small-angle neutron scattering studies and the second virial coefficient derived from sedimentation equilibrium analytical ultracentrifugation experiments.
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Affiliation(s)
- David J Scott
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, UK. .,Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxfordshire, OX11 0FA, UK. .,ISIS Spallation Neutron and Muon source, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxfordshire, OX11 0FA, UK.
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7
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Bellissent-Funel MC, Hassanali A, Havenith M, Henchman R, Pohl P, Sterpone F, van der Spoel D, Xu Y, Garcia AE. Water Determines the Structure and Dynamics of Proteins. Chem Rev 2016; 116:7673-97. [PMID: 27186992 DOI: 10.1021/acs.chemrev.5b00664] [Citation(s) in RCA: 517] [Impact Index Per Article: 64.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Water is an essential participant in the stability, structure, dynamics, and function of proteins and other biomolecules. Thermodynamically, changes in the aqueous environment affect the stability of biomolecules. Structurally, water participates chemically in the catalytic function of proteins and nucleic acids and physically in the collapse of the protein chain during folding through hydrophobic collapse and mediates binding through the hydrogen bond in complex formation. Water is a partner that slaves the dynamics of proteins, and water interaction with proteins affect their dynamics. Here we provide a review of the experimental and computational advances over the past decade in understanding the role of water in the dynamics, structure, and function of proteins. We focus on the combination of X-ray and neutron crystallography, NMR, terahertz spectroscopy, mass spectroscopy, thermodynamics, and computer simulations to reveal how water assist proteins in their function. The recent advances in computer simulations and the enhanced sensitivity of experimental tools promise major advances in the understanding of protein dynamics, and water surely will be a protagonist.
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Affiliation(s)
| | - Ali Hassanali
- International Center for Theoretical Physics, Condensed Matter and Statistical Physics 34151 Trieste, Italy
| | - Martina Havenith
- Ruhr-Universität Bochum , Faculty of Chemistry and Biochemistry Universitätsstraße 150 Building NC 7/72, D-44780 Bochum, Germany
| | - Richard Henchman
- Manchester Institute of Biotechnology The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Peter Pohl
- Johannes Kepler University , Gruberstrasse, 40 4020 Linz, Austria
| | - Fabio Sterpone
- Institut de Biologie Physico-Chimique Laboratoire de Biochimie Théorique 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - David van der Spoel
- Department of Cell and Molecular Biology, Computational and Systems Biology, Uppsala University , 751 24 Uppsala, Sweden
| | - Yao Xu
- Ruhr-Universität Bochum , Faculty of Chemistry and Biochemistry Universitätsstraße 150 Building NC 7/72, D-44780 Bochum, Germany
| | - Angel E Garcia
- Center for Non Linear Studies, Los Alamos National Laboratory , Los Alamos, New Mexico 87545, United States
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8
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Wills PR, Scott DJ, Winzor DJ. The osmotic second virial coefficient for protein self-interaction: Use and misuse to describe thermodynamic nonideality. Anal Biochem 2015; 490:55-65. [PMID: 26344712 DOI: 10.1016/j.ab.2015.08.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/13/2015] [Accepted: 08/14/2015] [Indexed: 11/16/2022]
Affiliation(s)
- Peter R Wills
- Department of Physics, University of Auckland, PB 92019, Auckland 1142, New Zealand.
| | - David J Scott
- Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Donald J Winzor
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
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9
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Scott DJ, Patel TR, Winzor DJ. A potential for overestimating the absolute magnitudes of second virial coefficients by small-angle X-ray scattering. Anal Biochem 2013; 435:159-65. [DOI: 10.1016/j.ab.2012.12.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 12/17/2012] [Accepted: 12/20/2012] [Indexed: 11/29/2022]
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10
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Siderius DW, Krekelberg WP, Roberts CJ, Shen VK. Osmotic virial coefficients for model protein and colloidal solutions: Importance of ensemble constraints in the analysis of light scattering data. J Chem Phys 2012; 136:175102. [DOI: 10.1063/1.4709613] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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11
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Patel TR, Besong TMD, Patel N, Meier M, Harding SE, Winzor DJ, Stetefeld J. Evidence for self-association of a miniaturized version of agrin from hydrodynamic and small-angle X-ray scattering measurements. J Phys Chem B 2011; 115:11286-93. [PMID: 21859138 DOI: 10.1021/jp206377b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydrodynamic studies of miniagrin indicate a molar mass that is 20% larger than the value calculated from the sequence of this genetically engineered protein. Consistent with this finding is the negative sign and also the magnitude of the second virial coefficient obtained from small-angle X-ray scattering measurements. The inference that miniagrin reversibly self-associates is confirmed by a sedimentation equilibrium study that yields an equilibrium constant of 0.24 L/g for a putative monomer-dimer interaction. Finally, Guinier analysis of the small-angle X-ray scattering (SAXS) results yields concentration-dependent values for the radius of gyration that may be described by the monomer-dimer model and respective R(g) values of 40 and 105 Å for the monomeric and dimeric miniagrin species. Although intermolecular protein interactions are endemic in the events leading to acetylcholine receptor aggregation by agrin, the matrix proteoglycan of which miniagrin is a miniaturized model, this investigation raises the possibility that agrin may itself self-associate.
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Affiliation(s)
- Trushar R Patel
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada.
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12
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Scott DJ, Patel TR, Besong DMT, Stetefeld J, Winzor DJ. Examination of the Discrepancy between Size Estimates for Ovalbumin from Small-Angle X-ray Scattering and Other Physicochemical Measurements. J Phys Chem B 2011; 115:10725-9. [DOI: 10.1021/jp2006149] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- David J. Scott
- National Center for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom
| | - Trushar R. Patel
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - David M. T. Besong
- National Center for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Donald J. Winzor
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
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13
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Saluja A, Fesinmeyer RM, Hogan S, Brems DN, Gokarn YR. Diffusion and sedimentation interaction parameters for measuring the second virial coefficient and their utility as predictors of protein aggregation. Biophys J 2011; 99:2657-65. [PMID: 20959107 DOI: 10.1016/j.bpj.2010.08.020] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 08/05/2010] [Accepted: 08/10/2010] [Indexed: 12/28/2022] Open
Abstract
The concentration-dependence of the diffusion and sedimentation coefficients (k(D) and k(s), respectively) of a protein can be used to determine the second virial coefficient (B₂), a parameter valuable in predicting protein-protein interactions. Accurate measurement of B₂ under physiologically and pharmaceutically relevant conditions, however, requires independent measurement of k(D) and k(s) via orthogonal techniques. We demonstrate this by utilizing sedimentation velocity (SV) and dynamic light scattering (DLS) to analyze solutions of hen-egg white lysozyme (HEWL) and a monoclonal antibody (mAb1) in different salt solutions. The accuracy of the SV-DLS method was established by comparing measured and literature B₂ values for HEWL. In contrast to the assumptions necessary for determining k(D) and k(s) via SV alone, k(D) and ks were of comparable magnitudes, and solution conditions were noted for both HEWL and mAb1 under which 1), k(D) and k(s) assumed opposite signs; and 2), k(D) ≥k(s). Further, we demonstrate the utility of k(D) and k(s) as qualitative predictors of protein aggregation through agitation and accelerated stability studies. Aggregation of mAb1 correlated well with B₂, k(D), and k(s), thus establishing the potential for k(D) to serve as a high-throughput predictor of protein aggregation.
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Affiliation(s)
- Atul Saluja
- Process and Product Development, Amgen, Seattle, Washington
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14
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The effect of glycosylation on interparticle interactions and dimensions of native and denatured phytase. Biophys J 2010; 96:153-61. [PMID: 18835893 DOI: 10.1529/biophysj.108.136408] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Glycosylation affects the physical properties of proteins in a number of ways including solubility and aggregation behavior. To elucidate the mechanism underlying these effects, we have measured second virial coefficients (A2) of the heavily glycosylated pheniophora lycii phytase (Phy) and its enzymatically deglycosylated counterpart (dgPhy) in native and in denatured form by means of small angle x-ray scattering. The measured A2-values show that the native forms of Phy and dgPhy are equally repulsive at the studied pH 8 where A2 equals 10.9 +/- 0.1 x 10(4) mL mol g(-2). However, when thermally denatured, the A2 of dgPhy decreases to 9.0 +/- 0.2 x 10(4) mL mol g(-2) whereas it remained unchanged for Phy. In accord with earlier investigations, the p(r)-function measured here suggested that the glycans did not affect the peptide structure of the native protein. Conversely, glycosylation markedly changed the structure of thermally denatured protein. This was evident from the radius of gyration, which increased by 32% for Phy and only 11% for dgPhy on denaturation. We suggest that this expanding effect of the glycans on the denatured protein conformation relies on steric hindrance that limits the range of torsion angles available to the polypeptide.
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15
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Gabrielsen M, Nagy LA, DeLucas LJ, Cogdell RJ. Self-interaction chromatography as a tool for optimizing conditions for membrane protein crystallization. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2009; 66:44-50. [PMID: 20057048 DOI: 10.1107/s0907444909043972] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Accepted: 10/23/2009] [Indexed: 11/11/2022]
Abstract
The second virial coefficient, or B value, is a measurement of how well a protein interacts with itself in solution. These interactions can lead to protein crystallization or precipitation, depending on their strength, with a narrow range of B values (the 'crystallization slot') being known to promote crystallization. A convenient method of determining the B value is by self-interaction chromatography. This paper describes how the light-harvesting complex 1-reaction centre core complex from Allochromatium vinosum yielded single straight-edged crystals after iterative cycles of self-interaction chromatography and crystallization. This process allowed the rapid screening of small molecules and detergents as crystallization additives. Here, a description is given of how self-interaction chromatography has been utilized to improve the crystallization conditions of a membrane protein.
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Affiliation(s)
- Mads Gabrielsen
- Division of Molecular and Cellular Biology, Faculty of Biological Life Sciences, University of Glasgow, Scotland
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16
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Tessier PM, Jinkoji J, Cheng YC, Prentice JL, Lenhoff AM. Self-Interaction Nanoparticle Spectroscopy: A Nanoparticle-Based Protein Interaction Assay. J Am Chem Soc 2008; 130:3106-12. [DOI: 10.1021/ja077624q] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Peter M. Tessier
- Center for Molecular and Engineering Thermodynamics, Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716
| | - Jun Jinkoji
- Center for Molecular and Engineering Thermodynamics, Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716
| | - Yu-Chia Cheng
- Center for Molecular and Engineering Thermodynamics, Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716
| | - Jessica L. Prentice
- Center for Molecular and Engineering Thermodynamics, Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716
| | - Abraham M. Lenhoff
- Center for Molecular and Engineering Thermodynamics, Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716
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17
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Tran HT, Pappu RV. Toward an accurate theoretical framework for describing ensembles for proteins under strongly denaturing conditions. Biophys J 2006; 91:1868-86. [PMID: 16766618 PMCID: PMC1544316 DOI: 10.1529/biophysj.106.086264] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2006] [Accepted: 05/31/2006] [Indexed: 11/18/2022] Open
Abstract
Our focus is on an appropriate theoretical framework for describing highly denatured proteins. In high concentrations of denaturants, proteins behave like polymers in a good solvent and ensembles for denatured proteins can be modeled by ignoring all interactions except excluded volume (EV) effects. To assay conformational preferences of highly denatured proteins, we quantify a variety of properties for EV-limit ensembles of 23 two-state proteins. We find that modeled denatured proteins can be best described as follows. Average shapes are consistent with prolate ellipsoids. Ensembles are characterized by large correlated fluctuations. Sequence-specific conformational preferences are restricted to local length scales that span five to nine residues. Beyond local length scales, chain properties follow well-defined power laws that are expected for generic polymers in the EV limit. The average available volume is filled inefficiently, and cavities of all sizes are found within the interiors of denatured proteins. All properties characterized from simulated ensembles match predictions from rigorous field theories. We use our results to resolve between conflicting proposals for structure in ensembles for highly denatured states.
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Affiliation(s)
- Hoang T Tran
- Department of Biomedical Engineering and Center for Computational Biology, Washington University in St. Louis, St. Louis, Missouri 63130-4899, USA
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18
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Ahamed T, Ottens M, van Dedem GWK, van der Wielen LAM. Design of self-interaction chromatography as an analytical tool for predicting protein phase behavior. J Chromatogr A 2005; 1089:111-24. [PMID: 16130779 DOI: 10.1016/j.chroma.2005.06.065] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Solution conditions under which proteins have a tendency to crystallize correspond to a slightly negative osmotic second virial coefficient (B22). A positive B22 value guarantees no crystallization to occur. On the other hand, a B22 value within the so called "crystallization slot" thermodynamically supports the crystallization processes but does not guarantee successful crystal growth. It is, however, a prerequisite for protein crystallization that the B22 value must be in the slightly negative regime. Self-interaction chromatography (SIC) is designed in this work as an analytical tool for determining B22 in a precise and reproducible way. The methodology was demonstrated in detail in terms of its theoretical basis, experimental methodology, troubleshooting and data analysis for different protein samples and solution conditions. The inherent error limit of SIC is found to be comparatively less than other B22 measurement techniques. The designed experimental approach was applied for mapping crystallization conditions of a model protein, i.e. lysozyme. Good agreement between the obtained lysozyme B22 values and literature values confirms the accuracy of the approach.
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Affiliation(s)
- Tangir Ahamed
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
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19
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Longhi S, Receveur-Bréchot V, Karlin D, Johansson K, Darbon H, Bhella D, Yeo R, Finet S, Canard B. The C-terminal domain of the measles virus nucleoprotein is intrinsically disordered and folds upon binding to the C-terminal moiety of the phosphoprotein. J Biol Chem 2003; 278:18638-48. [PMID: 12621042 DOI: 10.1074/jbc.m300518200] [Citation(s) in RCA: 230] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The nucleoprotein of measles virus consists of an N-terminal moiety, N(CORE), resistant to proteolysis and a C-terminal moiety, N(TAIL), hypersensitive to proteolysis and not visible as a distinct domain by electron microscopy. We report the bacterial expression, purification, and characterization of measles virus N(TAIL). Using nuclear magnetic resonance, circular dichroism, gel filtration, dynamic light scattering, and small angle x-ray scattering, we show that N(TAIL) is not structured in solution. Its sequence and spectroscopic and hydrodynamic properties indicate that N(TAIL) belongs to the premolten globule subfamily within the class of intrinsically disordered proteins. The same epitopes are exposed in N(TAIL) and within the nucleoprotein, which rules out dramatic conformational changes in the isolated N(TAIL) domain compared with the full-length nucleoprotein. Most unstructured proteins undergo some degree of folding upon binding to their partners, a process termed "induced folding." We show that N(TAIL) is able to bind its physiological partner, the phosphoprotein, and that it undergoes such an unstructured-to-structured transition upon binding to the C-terminal moiety of the phosphoprotein. The presence of flexible regions at the surface of the viral nucleocapsid would enable plastic interactions with several partners, whereas the gain of structure arising from induced folding would lead to modulation of these interactions. These results contribute to the study of the emerging field of natively unfolded proteins.
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Affiliation(s)
- Sonia Longhi
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS et Université Aix-Marseille I et II, ESIL, Campus de Luminy, 13288 Marseille Cedex 09, France.
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20
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Receveur V, Czjzek M, Schülein M, Panine P, Henrissat B. Dimension, shape, and conformational flexibility of a two domain fungal cellulase in solution probed by small angle X-ray scattering. J Biol Chem 2002; 277:40887-92. [PMID: 12186865 DOI: 10.1074/jbc.m205404200] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellulase Cel45 from Humicola insolens has a modular structure with a catalytic module and a cellulose-binding module (CBM) separated by a 36 amino acid, glycosylated, linker peptide. The solution conformation of the entire two domain Cel45 protein as well as the effect of the length and flexibility of the linker on the spatial arrangement of the constitutive modules were studied by small angle x-ray scattering combined with the known three-dimensional structure of the individual modules. The measured dimensions of the enzyme show that the linker exhibits an extended conformation leading to a maximum extension between the two centers of mass of each module corresponding to about four cellobiose units on a cellulose chain. The glycosylation of the linker is the key factor defining its extended conformation, and a five proline stretch mutation on the linker was found to confer a higher rigidity to the enzyme. Our study shows that the respective positioning of the catalytic module and the CBM onto the insoluble substrate is most likely influenced by the linker structure and flexibility. Our results are consistent with a model where cellulases can move on the surface of cellulose with a caterpillar-like displacement with free energy restrictions.
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Affiliation(s)
- Véronique Receveur
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098, CNRS and Universités d'Aix-Marseille I and II, 31 Chemin Joseph Aiguier, 13402 Marseille cedex 20, France.
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21
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Gall A, Seguin J, Robert B, Bellissent-Funel MC. Membrane Proteins in Bulk Solution Can Be Used for Quasi-Elastic Neutron Scattering Studies: The Case for the Photochemical Reaction Center. J Phys Chem B 2002. [DOI: 10.1021/jp014079l] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrew Gall
- Laboratoire Léon Brillouin (CEA-CNRS), CEA-Saclay, 91191 Gif-sur-Yvette Cedex, France, and Service de Biophysique des Fonctions Membranaires, DBJC/CEA and URA CNRS 2096, CEA-Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Jérôme Seguin
- Laboratoire Léon Brillouin (CEA-CNRS), CEA-Saclay, 91191 Gif-sur-Yvette Cedex, France, and Service de Biophysique des Fonctions Membranaires, DBJC/CEA and URA CNRS 2096, CEA-Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Bruno Robert
- Laboratoire Léon Brillouin (CEA-CNRS), CEA-Saclay, 91191 Gif-sur-Yvette Cedex, France, and Service de Biophysique des Fonctions Membranaires, DBJC/CEA and URA CNRS 2096, CEA-Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Marie-Claire Bellissent-Funel
- Laboratoire Léon Brillouin (CEA-CNRS), CEA-Saclay, 91191 Gif-sur-Yvette Cedex, France, and Service de Biophysique des Fonctions Membranaires, DBJC/CEA and URA CNRS 2096, CEA-Saclay, 91191 Gif-sur-Yvette Cedex, France
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22
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Tessier PM, Lenhoff AM, Sandler SI. Rapid measurement of protein osmotic second virial coefficients by self-interaction chromatography. Biophys J 2002; 82:1620-31. [PMID: 11867474 PMCID: PMC1301960 DOI: 10.1016/s0006-3495(02)75513-6] [Citation(s) in RCA: 179] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Weak protein interactions are often characterized in terms of the osmotic second virial coefficient (B(22)), which has been shown to correlate with protein phase behavior, such as crystallization. Traditional methods for measuring B(22), such as static light scattering, are too expensive in terms of both time and protein to allow extensive exploration of the effects of solution conditions on B(22). In this work we have measured protein interactions using self-interaction chromatography, in which protein is immobilized on chromatographic particles and the retention of the same protein is measured in isocratic elution. The relative retention of the protein reflects the average protein interactions, which we have related to the second virial coefficient via statistical mechanics. We obtain quantitative agreement between virial coefficients measured by self-interaction chromatography and traditional characterization methods for both lysozyme and chymotrypsinogen over a wide range of pH and ionic strengths, yet self-interaction chromatography requires at least an order of magnitude less time and protein than other methods. The method thus holds significant promise for the characterization of protein interactions requiring only commonly available laboratory equipment, little specialized expertise, and relatively small investments of both time and protein.
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Affiliation(s)
- Peter M Tessier
- Center for Molecular and Engineering Thermodynamics, Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716, USA
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23
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Kundrotas PJ, Karshikoff A. Model for calculation of electrostatic interactions in unfolded proteins. PHYSICAL REVIEW E 2002; 65:011901. [PMID: 11800712 DOI: 10.1103/physreve.65.011901] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2001] [Indexed: 11/07/2022]
Abstract
An approach for the calculation of electrostatic interactions and titration properties of unfolded polypeptide chains (denatured proteins) is proposed. It is based on a simple representation of the denatured proteins as a state with titratable sites distributed on the surface of a sphere, radius of which is assumed to be equal to the radius of gyration, R(g), of an unfolded molecule. Distances between the charges, d, obey constraints arising from the protein sequence. Criteria for evaluation of the parameters R(g) and d were obtained from computer simulations on a polypeptide consisting of 20 identical amino acids (polylysine). The model was applied for calculation of titration curves of denatured barnase and staphylococcal nuclease. It was demonstrated that the approach proposed gives considerably better agreement with the experimental data than the commonly used null approximation. It was also found that titration properties of denatured proteins are slightly, but distinguishably influenced by the amino-acid sequence of the protein.
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Affiliation(s)
- P J Kundrotas
- Department of Biosciences at Novum Research Park, Karolinska Institutet, SE-141 57 Huddinge, Stockholm, Sweden
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24
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Russo D, Durand D, Calmettes P, Desmadril M. Characterization of the denatured states distribution of neocarzinostatin by small-angle neutron scattering and differential scanning calorimetry. Biochemistry 2001; 40:3958-66. [PMID: 11300776 DOI: 10.1021/bi002200t] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The denatured states of a small globular protein, apo-neocarzinostatin (NCS), have been characterized using several techniques. Structural properties were investigated by optical spectroscopy techniques and small-angle neutron scattering (SANS), as a function of guanidinium chloride (GdmCl) concentration. SANS experiments show that in heavy water, the protein keeps its native size at GdmCl concentrations below 2.5 M. A sharp transition occurs at about 3.6 M GdmCl, and NCS behaves like an excluded volume chain above 5 M. The same behavior is observed in deuterated buffer by fluorescence and circular dichroism measurements. For the H(2)O buffer, the transition occurs with lower concentration of denaturant, the shift being about 0.6 M. 8-Anilino-1-naphthalenesulfonate (ANS) was used as a hydrophobic fluorescent probe for studying the early stages of protein unfolding. Protein denaturation modifies the fluorescence intensity of ANS, a maximum of intensity being detected close to 2 M GdmCl in hydrogenated buffer, which shows the existence of at least one intermediate state populated at the beginning of the unfolding pathway. Differential scanning calorimetry (DSC) was used to obtain thermodynamic values for NCS denaturation. The melting curves recorded between 20 and 90 degrees C in the presence of various GdmCl concentrations (0-3 M) cannot be explained by a simple two-state model. Altogether, the data presented in this paper suggest that before unfolding the protein explores a distribution of states which is centered around compact states at denaturant concentrations below 2 M in H(2)O, and then shifts to less structured states by increasing denaturant concentrations.
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Affiliation(s)
- D Russo
- Laboratoire Léon Brillouin, CE-Saclay, 91191 Gif-sur-Yvette Cedex, France
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25
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Haldar J, Aswal VK, Goyal PS, Bhattacharya S. Molecular Modulation of Surfactant Aggregation in Water: Effect of the Incorporation of Multiple Headgroups on Micellar Properties. Angew Chem Int Ed Engl 2001. [DOI: 10.1002/1521-3773(20010401)40:7<1228::aid-anie1228>3.0.co;2-i] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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26
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Haldar J, Aswal VK, Goyal PS, Bhattacharya S. Molekulare Modulation der Aggregation von Tensiden in Wasser: Einfluss des Einbaus mehrerer Kopfgruppen auf die Micelleneigenschaften. Angew Chem Int Ed Engl 2001. [DOI: 10.1002/1521-3757(20010401)113:7<1278::aid-ange1278>3.0.co;2-l] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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27
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Gall A, Dellerue S, Lapouge K, Robert B, Bellissent-Funel MC. Small angle neutron scattering measurements on the membrane protein subunit B777 in a detergent microemulsion. Biopolymers 2001; 58:231-4. [PMID: 11169383 DOI: 10.1002/1097-0282(200103)58:3<231::aid-bip1000>3.0.co;2-#] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- A Gall
- Laboratoire Léon Brillouin (CEA-CNRS), CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France.
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28
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Abstract
Cold denaturation of yeast phosphoglycerate kinase (yPGK) was investigated by a combination of far UV circular dichroism (CD), steady-state and time-resolved fluorescence, and small angle X-ray scattering. It was shown that cold denaturation of yPGK cannot be accounted for by a simple two-state process and that an intermediate state can be stabilized under mild denaturing conditions. Comparison between far UV CD and fluorescence shows that in this state the protein displays a fluorescence signal corresponding mainly to exposed tryptophans, whereas its CD signal is only partially modified. Comparison with spectroscopic data obtained from a mutant missing the last 12 amino-acids (yPGK delta404) suggests that lowering the temperature mainly results in a destabilization of hydrophobic interactions between the two domains. Small angle X-ray scattering measurements give further information about this stabilized intermediate. At 4 degrees C and in the presence of 0.45 M Gdn-HCl, the main species corresponds to a protein as compact as native yPGK, whereas a significant proportion of ellipticity has been lost. Although various techniques have shown the existence of residual structures in denatured proteins, this is one example of a compact denatured state devoid of its main content in alpha helices.
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Affiliation(s)
- V Receveur
- Laboratoire de Modélisation et Ingénierie des Protéines, Université de Paris-Sud Orsay, France
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29
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Wilkins DK, Grimshaw SB, Receveur V, Dobson CM, Jones JA, Smith LJ. Hydrodynamic radii of native and denatured proteins measured by pulse field gradient NMR techniques. Biochemistry 1999; 38:16424-31. [PMID: 10600103 DOI: 10.1021/bi991765q] [Citation(s) in RCA: 769] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Pulse field gradient NMR methods have been used to determine the effective hydrodynamic radii of a range of native and nonnative protein conformations. From these experimental data, empirical relationships between the measured hydrodynamic radius (R(h)) and the number of residues in the polypeptide chain (N) have been established; for native folded proteins R(h) = 4.75N (0.29)A and for highly denatured states R(h) = 2.21N (0.57)A. Predictions from these equations agree well with experimental data from dynamic light scattering and small-angle X-ray or neutron scattering studies reported in the literature for proteins ranging in size from 58 to 760 amino acid residues. The predicted values of the hydrodynamic radii provide a framework that can be used to analyze the conformational properties of a range of nonnative states of proteins. Several examples are given here to illustrate this approach including data for partially structured molten globule states and for proteins that are unfolded but biologically active under physiological conditions. These reveal evidence for significant coupling between local and global features of the conformational ensembles adopted in such states. In particular, the effective dimensions of the polypeptide chain are found to depend significantly on the level of persistence of regions of secondary structure or features such as hydrophobic clusters within a conformational ensemble.
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Affiliation(s)
- D K Wilkins
- Oxford Centre for Molecular Sciences, New Chemistry Laboratory, University of Oxford, England
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