1
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Arakawa T, Tomioka Y, Akuta T, Shiraki K. The contrasting roles of co-solvents in protein formulations and food products. Biophys Chem 2024; 312:107282. [PMID: 38944944 DOI: 10.1016/j.bpc.2024.107282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/29/2024] [Accepted: 06/14/2024] [Indexed: 07/02/2024]
Abstract
Protein aggregation is a major hurdle in developing biopharmaceuticals, in particular protein formulation area, but plays a pivotal role in food products. Co-solvents are used to suppress protein aggregation in pharmaceutical proteins. On the contrary, aggregation is encouraged in the process of food product making. Thus, it is expected that co-solvents play a contrasting role in biopharmaceutical formulation and food products. Here, we show several examples that utilize co-solvents, e.g., salting-out salts, sugars, polyols and divalent cations in promoting protein-protein interactions. The mechanisms of co-solvent effects on protein aggregation and solubility have been studied on aqueous protein solution and applied to develop pharmaceutical formulation based on the acquired scientific knowledge. On the contrary, co-solvents have been used in food industries based on empirical basis. Here, we will review the mechanisms of co-solvent effects on protein-protein interactions that can be applied to both pharmaceutical and food industries and hope to convey knowledge acquired through research on co-solvent interactions in aqueous protein solution and formulation to those involved in food science and provide those involved in protein solution research with the observations on aggregation behavior of food proteins.
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Affiliation(s)
- Tsutomu Arakawa
- Alliance Protein Laboratories, 13380 Pantera Road, San Diego, CA 92130, USA.
| | - Yui Tomioka
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd, 3333-26, Aza-Asayama, Kamitezuna Tahahagi, Ibaraki 318-0004, Japan
| | - Teruo Akuta
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd, 3333-26, Aza-Asayama, Kamitezuna Tahahagi, Ibaraki 318-0004, Japan
| | - Kentaro Shiraki
- Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
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2
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Senft MD, Maier R, Hiremath A, Zhang F, Schreiber F. Effective interactions and phase behavior of protein solutions in the presence of hexamine cobalt(III) chloride. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:119. [PMID: 38051398 PMCID: PMC10698144 DOI: 10.1140/epje/s10189-023-00376-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/09/2023] [Indexed: 12/07/2023]
Abstract
It is well established that deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) exhibit a reentrant condensation (RC) phase behavior in the presence of the trivalent hexamine cobalt(III) cations (Hac) which can be important for their packing and folding. A similar behavior can be observed for negatively charged globular proteins in the presence of trivalent metal cations, such as Y3+ or La3+. This phase behavior is mainly driven by charge inversion upon an increasing salt concentration for a fixed protein concentration (cp). However, as Hac exhibits structural differences compared to other multivalent metal cations, with six ammonia ligands (NH3) covalently bonded to the central cobalt atom, it is not clear that Hac can induce a similar phase behavior for proteins. In this work, we systematically investigate whether negatively charged globular proteins β-lactoglobulin (BLG), bovine serum albumin (BSA), human serum albumin (HSA) and ovalbumin (OVA) feature Hac-induced RC. Effective protein-protein interactions were investigated by small-angle X-ray scattering. The reduced second virial coefficient (B2/B2HS) was obtained as a function of salt concentration. The virial coefficient analysis performed confirms the reentrant interaction (RI) behavior for BLG without actually inducing RC, given the insufficient strengths of the interactions for the latter to occur. In contrast, the strength of attraction for BSA, HSA and OVA are too weak to show RC. Model free analysis of the inverse intensity [Formula: see text] also supports this finding. Looking at different q-range by employing static (SLS) and dynamic light scattering experiments, the presence of RI behavior can be confirmed. The results are further discussed in view of metal cation binding sites in nucleic acids (DNA and RNA), where Hac induced RC phase behavior.
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Affiliation(s)
- Maximilian D Senft
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany.
| | - Ralph Maier
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Anusha Hiremath
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany.
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
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3
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Philo JS. SEDNTERP: a calculation and database utility to aid interpretation of analytical ultracentrifugation and light scattering data. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:233-266. [PMID: 36792822 DOI: 10.1007/s00249-023-01629-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 02/17/2023]
Abstract
Proper interpretation of analytical ultracentrifugation (AUC) data for purified proteins requires ancillary information and calculations to account for factors such as buoyancy, buffer viscosity, hydration, and temperature. The utility program SEDNTERP has been widely used by the AUC community for this purpose since its introduction in the mid-1990s. Recent extensions to this program (1) allow it to incorporate data from diffusion as well as AUC experiments; and (2) allow it to calculate the refractive index of buffer solutions (based on the solute composition of the buffer), as well as the specific refractive increment (dn/dc) of proteins based on their composition. These two extensions should be quite useful to the light scattering community as well as helpful for AUC users. The latest version also adds new terms to the partial specific volume calculations which should improve the accuracy, particularly for smaller proteins and peptides, and can calculate the viscosity of buffers containing heavy isotopes of water. It also uses newer, more accurate equations for the density of water and for the hydrodynamic properties of rods and disks. This article will summarize and review all the equations used in the current program version and the scientific background behind them. It will tabulate the values used to calculate the partial specific volume and dn/dc, as well as the polynomial coefficients used in calculating the buffer density and viscosity (most of which have not been previously published), as well as the new ones used in calculating the buffer refractive index.
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Affiliation(s)
- John S Philo
- Alliance Protein Laboratories, San Diego, CA, USA.
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4
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Beck C, Grimaldo M, Lopez H, Da Vela S, Sohmen B, Zhang F, Oettel M, Barrat JL, Roosen-Runge F, Schreiber F, Seydel T. Short-Time Transport Properties of Bidisperse Suspensions of Immunoglobulins and Serum Albumins Consistent with a Colloid Physics Picture. J Phys Chem B 2022; 126:7400-7408. [PMID: 36112146 PMCID: PMC9527755 DOI: 10.1021/acs.jpcb.2c02380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The crowded environment of biological systems such as
the interior
of living cells is occupied by macromolecules with a broad size distribution.
This situation of polydispersity might influence the dependence of
the diffusive dynamics of a given tracer macromolecule in a monodisperse
solution on its hydrodynamic size and on the volume fraction. The
resulting size dependence of diffusive transport crucially influences
the function of a living cell. Here, we investigate a simplified model
system consisting of two constituents in aqueous solution, namely,
of the proteins bovine serum albumin (BSA) and bovine polyclonal gamma-globulin
(Ig), systematically depending on the total volume fraction and ratio
of these constituents. From high-resolution quasi-elastic neutron
spectroscopy, the separate apparent short-time diffusion coefficients
for BSA and Ig in the mixture are extracted, which show substantial
deviations from the diffusion coefficients measured in monodisperse
solutions at the same total volume fraction. These deviations can
be modeled quantitatively using results from the short-time rotational
and translational diffusion in a two-component hard sphere system
with two distinct, effective hydrodynamic radii. Thus, we find that
a simple colloid picture well describes short-time diffusion in binary
mixtures as a function of the mixing ratio and the total volume fraction.
Notably, the self-diffusion of the smaller protein BSA in the mixture
is faster than the diffusion in a pure BSA solution, whereas the self-diffusion
of Ig in the mixture is slower than in the pure Ig solution.
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Affiliation(s)
- Christian Beck
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
- Institut Max von Laue─Paul Langevin (ILL), CS 20156, F-38042 Grenoble Cedex 9, France
| | - Marco Grimaldo
- Institut Max von Laue─Paul Langevin (ILL), CS 20156, F-38042 Grenoble Cedex 9, France
| | - Hender Lopez
- School of Physics and Optometric & Clinical Sciences, Technological University Dublin, D07 XT95 Grangegorman, Ireland
| | - Stefano Da Vela
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Benedikt Sohmen
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Martin Oettel
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | | | - Felix Roosen-Runge
- Department of Biomedical Science and Biofilms-Research Center for Biointerfaces (BRCB), Malmö University, 20506 Malmö, Sweden
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Tilo Seydel
- Institut Max von Laue─Paul Langevin (ILL), CS 20156, F-38042 Grenoble Cedex 9, France
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Temporal and spatial characterisation of protein liquid-liquid phase separation using NMR spectroscopy. Nat Commun 2022; 13:1767. [PMID: 35365630 PMCID: PMC8976059 DOI: 10.1038/s41467-022-29408-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 03/11/2022] [Indexed: 12/15/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) of protein solutions is increasingly recognised as an important phenomenon in cell biology and biotechnology. However, opalescence and concentration fluctuations render LLPS difficult to study, particularly when characterising the kinetics of the phase transition and layer separation. Here, we demonstrate the use of a probe molecule trifluoroethanol (TFE) to characterise the kinetics of protein LLPS by NMR spectroscopy. The chemical shift and linewidth of the probe molecule are sensitive to local protein concentration, with this sensitivity resulting in different characteristic signals arising from the dense and lean phases. Monitoring of these probe signals by conventional bulk-detection 19F NMR reports on the formation and evolution of both phases throughout the sample, including their concentrations and volumes. Meanwhile, spatially-selective 19F NMR, in which spectra are recorded from smaller slices of the sample, was used to track the distribution of the different phases during layer separation. This experimental strategy enables comprehensive characterisation of the process and kinetics of LLPS, and may be useful to study phase separation in protein systems as a function of their environment.
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6
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Nishinami S, Arakawa T, Shiraki K. Classification of protein solubilizing additives by fluorescence assay. Int J Biol Macromol 2022; 203:695-702. [PMID: 35090940 DOI: 10.1016/j.ijbiomac.2022.01.137] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 11/17/2022]
Abstract
Aromatic interaction plays a crucial role in controlling protein interaction by additives. Here we investigated the interaction of protein salting-in (solubilizing) additives with tryptophan (Trp), tyrosine (Tyr), indole, and proteins based on their fluorescence spectra. Five salting-in additives, i.e., arginine (Arg), urea, guanidine (Gdn), ethylene glycol (EG), and magnesium chloride (MgCl2), showed different effects on the fluorescence properties of Trp and Tyr. Arg significantly reduced fluorescence intensity of Trp and Tyr, as was the case for glycine to a lesser extent. MgCl2 and calcium chloride (CaCl2) showed little effect on the aromatic fluorescence spectra. Gdn also showed little effect on the aromatic fluorescence spectra of Trp and Tyr even at high concentrations. EG increased the aromatic fluorescence intensity of Trp and Tyr with blue-shifted emission wavelength. Urea enhanced fluorescence of Trp and Tyr without altering emission wavelength. These results indicate that the protein solubilizing additives interact with aromatic groups differently.
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Affiliation(s)
- Suguru Nishinami
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Tsutomu Arakawa
- Alliance Protein Laboratories, San Diego, CA 92130, United States
| | - Kentaro Shiraki
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan.
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7
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Insight into the protein salting-in mechanism of arginine, magnesium chloride and ethylene glycol: Solvent interaction with aromatic solutes. Int J Biol Macromol 2021; 188:670-677. [PMID: 34400229 DOI: 10.1016/j.ijbiomac.2021.08.070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/01/2021] [Accepted: 08/09/2021] [Indexed: 11/18/2022]
Abstract
Key factors in the salting-in effects on proteins of additives are their interactions with aromatic groups. We studied the interaction of four aromatic solutes, benzyl alcohol (BA), phenol, 4-hydroxybenzyl alcohol (4-HBA) and methyl gallate (MG), with different salting-in additives, arginine hydrochloride (ArgHCl), magnesium chloride (MgCl2), ethylene glycol (EG), and guanidine hydrochloride (GdnHCl) using solubility measurements. We used sodium chloride (NaCl) as a control. MgCl2 decreased the solubility of the four aromatic solutes with weak solute dependence. In contrast, ArgHCl, GdnHCl, and EG increased the solubility of four aromatic solutes with a similar solute dependence. Their salting-in effects were weaker on BA and 4-HBA and stronger on phenol and MG. These results indicate that attached groups alter the aromatic properties, affecting the interactions between the benzene ring and these three additives. More importantly, the observed results demonstrate that the salting-in mechanism is different between MgCl2, EG and ArgHCl, which should play a role in their effects on protein solubility.
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8
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Aune K, Lee J, Prakash V, Bhat R, Andreu J, Monasterio O, Perez-Ramirez B, Shearwin K, Arakawa T, Carpenter J, Crowe J, Crowe L, Somero G, Gagnon P, Charles MT. A tribute to Dr. Serge N. Timasheff, our mentor. Biophys Rev 2021; 13:459-484. [PMID: 34471434 PMCID: PMC8355303 DOI: 10.1007/s12551-021-00814-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 06/17/2021] [Indexed: 10/20/2022] Open
Abstract
Dr. Serge N. Timasheff, our mentor and friend, passed away in 2019. This article is a collection of tributes from his postdoctoral fellows, friends, and daughter, who all have been associated with or influenced by him or his research. Dr. Timasheff is a pioneer of research on thermodynamic linkage between ligand interaction and macromolecular reaction. We all learned a great deal from Dr. Timasheff, not only about science but also about life.
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Affiliation(s)
- Kirk Aune
- 7647 Cortana Drive, Granger, IN 46530 USA
| | - James Lee
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77059 USA
| | - V. Prakash
- Nutraceuticals and Nutritional Research Center, Ramaiah University of Applied Sciences, Bangalore, India
| | - Rajiv Bhat
- School of Biotechnology, Jawaharalal Nehru University, New Delhi, 110067 India
| | - Jose Andreu
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Octavio Monasterio
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Bernardo Perez-Ramirez
- CMC-Drug Device Integration, DP-Due Diligence, Biologics Drug Product Development & Manufacturing, Sanofi, 1 the Mountain Road, Framingham, MA 01701 USA
| | - Keith Shearwin
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, 5005 Australia
| | - Tsutomu Arakawa
- Alliance Protein Laboratories, 13380 Pantera Road, San Diego, CA 92130 USA
| | - John Carpenter
- Department of Pharmaceutical Sciences, Center for Pharmaceutical Biotechnology, University of Colorado Anshutz Medical Campus, Auroa, CO 80045 USA
| | - John Crowe
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616 USA
| | - Lois Crowe
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616 USA
| | - George Somero
- Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950 USA
| | - Pete Gagnon
- BIA Separations, Mirce 21, 5270, Ajdovscina, Slovenia
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9
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Reyes-Aldrete E, Dill EA, Bussetta C, Szymanski MR, Diemer G, Maindola P, White MA, Bujalowski WM, Choi KH, Morais MC. Biochemical and Biophysical Characterization of the dsDNA Packaging Motor from the Lactococcus lactis Bacteriophage Asccphi28. Viruses 2020; 13:E15. [PMID: 33374840 PMCID: PMC7823558 DOI: 10.3390/v13010015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/16/2020] [Accepted: 12/16/2020] [Indexed: 02/07/2023] Open
Abstract
Double-stranded DNA viruses package their genomes into pre-assembled protein procapsids. This process is driven by macromolecular motors that transiently assemble at a unique vertex of the procapsid and utilize homomeric ring ATPases to couple genome encapsidation to ATP hydrolysis. Here, we describe the biochemical and biophysical characterization of the packaging ATPase from Lactococcus lactis phage asccφ28. Size-exclusion chromatography (SEC), analytical ultracentrifugation (AUC), small angle X-ray scattering (SAXS), and negative stain transmission electron microscopy (TEM) indicate that the ~45 kDa protein formed a 443 kDa cylindrical assembly with a maximum dimension of ~155 Å and radius of gyration of ~54 Å. Together with the dimensions of the crystallographic asymmetric unit from preliminary X-ray diffraction experiments, these results indicate that gp11 forms a decameric D5-symmetric complex consisting of two pentameric rings related by 2-fold symmetry. Additional kinetic analysis shows that recombinantly expressed gp11 has ATPase activity comparable to that of functional ATPase rings assembled on procapsids in other genome packaging systems. Hence, gp11 forms rings in solution that likely reflect the fully assembled ATPases in active virus-bound motor complexes. Whereas ATPase functionality in other double-stranded DNA (dsDNA) phage packaging systems requires assembly on viral capsids, the ability to form functional rings in solution imparts gp11 with significant advantages for high-resolution structural studies and rigorous biophysical/biochemical analysis.
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Affiliation(s)
- Emilio Reyes-Aldrete
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
| | - Erik A. Dill
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
| | - Cecile Bussetta
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
| | - Michal R. Szymanski
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
| | - Geoffrey Diemer
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
| | - Priyank Maindola
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
| | - Mark A. White
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Wlodzimierz M. Bujalowski
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Kyung H. Choi
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Marc C. Morais
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
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10
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Wood VE, Groves K, Cryar A, Quaglia M, Matejtschuk P, Dalby PA. HDX and In Silico Docking Reveal that Excipients Stabilize G-CSF via a Combination of Preferential Exclusion and Specific Hotspot Interactions. Mol Pharm 2020; 17:4637-4651. [PMID: 33112626 DOI: 10.1021/acs.molpharmaceut.0c00877] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Assuring the stability of therapeutic proteins is a major challenge in the biopharmaceutical industry, and a better molecular understanding of the mechanisms through which formulations influence their stability is an ongoing priority. While the preferential exclusion effects of excipients are well known, the additional presence and impact of specific protein-excipient interactions have proven to be more elusive to identify and characterize. We have taken a combined approach of in silico molecular docking and hydrogen deuterium exchange-mass spectrometry (HDX-MS) to characterize the interactions between granulocyte colony-stimulating factor (G-CSF), and some common excipients. These interactions were related to their influence on the thermal-melting temperatures (Tm) for the nonreversible unfolding of G-CSF in liquid formulations. The residue-level interaction sites predicted in silico correlated well with those identified experimentally and highlighted the potential impact of specific excipient interactions on the Tm of G-CSF.
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Affiliation(s)
- Victoria E Wood
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Kate Groves
- National Measurement Laboratory at LGC Ltd., Queens Road, Teddington TW11 0LY, United Kingdom
| | - Adam Cryar
- National Measurement Laboratory at LGC Ltd., Queens Road, Teddington TW11 0LY, United Kingdom
| | - Milena Quaglia
- National Measurement Laboratory at LGC Ltd., Queens Road, Teddington TW11 0LY, United Kingdom
| | - Paul Matejtschuk
- National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, United Kingdom
| | - Paul A Dalby
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, United Kingdom
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11
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Holstein M, Hung J, Feroz H, Ranjan S, Du C, Ghose S, Li ZJ. Strategies for high‐concentration drug substance manufacturing to facilitate subcutaneous administration: A review. Biotechnol Bioeng 2020; 117:3591-3606. [DOI: 10.1002/bit.27510] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/17/2020] [Accepted: 07/18/2020] [Indexed: 12/27/2022]
Affiliation(s)
- Melissa Holstein
- Biologics Process Development, Global Product Development and Supply Bristol‐Myers Squibb Co. Devens Massachusetts
| | - Jessica Hung
- Biologics Process Development, Global Product Development and Supply Bristol‐Myers Squibb Co. Devens Massachusetts
| | - Hasin Feroz
- Biologics Process Development, Global Product Development and Supply Bristol‐Myers Squibb Co. Devens Massachusetts
| | - Swarnim Ranjan
- Biologics Process Development, Global Product Development and Supply Bristol‐Myers Squibb Co. Devens Massachusetts
| | - Cheng Du
- Biologics Process Development, Global Product Development and Supply Bristol‐Myers Squibb Co. Devens Massachusetts
| | - Sanchayita Ghose
- Biologics Process Development, Global Product Development and Supply Bristol‐Myers Squibb Co. Devens Massachusetts
| | - Zheng Jian Li
- Biologics Process Development, Global Product Development and Supply Bristol‐Myers Squibb Co. Devens Massachusetts
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12
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Uttinger MJ, Heyn TR, Jandt U, Wawra SE, Winzer B, Keppler JK, Peukert W. Measurement of length distribution of beta-lactoglobulin fibrils by multiwavelength analytical ultracentrifugation. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:745-760. [PMID: 32006057 PMCID: PMC7701075 DOI: 10.1007/s00249-020-01421-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/19/2019] [Accepted: 01/03/2020] [Indexed: 11/24/2022]
Abstract
The whey protein beta-lactoglobulin is the building block of amyloid fibrils which exhibit a great potential in various applications. These include stabilization of gels or emulsions. During biotechnological processing, high shear forces lead to fragmentation of fibrils and therefore to smaller fibril lengths. To provide insight into such processes, pure straight amyloid fibril dispersions (prepared at pH 2) were produced and sheared using the rotor stator setup of an Ultra Turrax. In the first part of this work, the sedimentation properties of fragmented amyloid fibrils sheared at different stress levels were analyzed with mulitwavelength analytical ultracentrifugation (AUC). Sedimentation data analysis was carried out with the boundary condition that fragmented fibrils were of cylindrical shape, for which frictional properties are known. These results were compared with complementary atomic force microscopy (AFM) measurements. We demonstrate how the sedimentation coefficient distribution from AUC experiments is influenced by the underlying length and diameter distribution of amyloid fibrils. In the second part of this work, we show how to correlate the fibril size reduction kinetics with the applied rotor revolution and the resulting energy density, respectively, using modal values of the sedimentation coefficients obtained from AUC. Remarkably, the determined scaling laws for the size reduction are in agreement with the results for other material systems, such as emulsification processes or the size reduction of graphene oxide sheets.
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Affiliation(s)
- Maximilian J Uttinger
- Institute of Particle Technology, Interdisciplinary Center for Functional Particle Systems, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Timon R Heyn
- Institute of Human Nutrition and Food Science, Division of Food Technology, Kiel University, 24118, Kiel, Germany
| | - Uwe Jandt
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany
| | - Simon E Wawra
- Institute of Particle Technology, Interdisciplinary Center for Functional Particle Systems, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Bettina Winzer
- Institute of Particle Technology, Interdisciplinary Center for Functional Particle Systems, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Julia K Keppler
- Institute of Human Nutrition and Food Science, Division of Food Technology, Kiel University, 24118, Kiel, Germany.,Laboratory of Food Process Engineering, Wageningen University, Bornse Weilanden 9, 6708WG, Wageningen, P.O. Box 17, 6700 AA, Wageningen, The Netherlands
| | - Wolfgang Peukert
- Institute of Particle Technology, Interdisciplinary Center for Functional Particle Systems, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
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13
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Miyawaki O. Solution thermodynamic approach to analyze protein stability in aqueous solutions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140256. [PMID: 31352058 DOI: 10.1016/j.bbapap.2019.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 07/23/2019] [Indexed: 12/01/2022]
Abstract
Protein thermal stability was analyzed by a solution thermodynamic approach. The small energetic differences in hydrogen-bonds (HB) among amino acid resdues and water molecules were proved to be amplified by the large number of HB involved to bring about the equilibrium shift from folding to unfolding of proteins. In aqueous solutions, water activity (Aw) plays a key role in protein stability. Therefore, Aw was precisely determined for various solutions and its relationship with solution structure was discussed. Wyman-Tanford analysis based on Aw showed linear regressions, without exception, between protein unfolding-ratio and Aw for lysozyme, ribonuclease A, and α-chymotrypsinogen A in various solutions with sugars, osmolytes, alcohols, and protein denaturant. From this linear regression, the free energy difference, ΔΔG, for a protein in a solution and in pure water, was easily obtained. Protein stability in a solution was proved to be determined by a balance between hydration and solute-binding effects to the protein and also by solution structure, which indirectly affects the hydrophobic interaction in a protein molecule. Temperature dependence of HB on protein stability suggested its interrelationship with hydrophobic interaction.
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Affiliation(s)
- Osato Miyawaki
- Department of Food Science, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan.
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14
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Thermodynamics of protein folding: methodology, data analysis and interpretation of data. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:305-316. [DOI: 10.1007/s00249-019-01362-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 12/10/2018] [Accepted: 03/18/2019] [Indexed: 01/17/2023]
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15
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Arakawa T, Kita Y. Protein Solvent Interaction: Transition of Protein-solvent Interaction Concept from Basic Research into Solvent Manipulation of Chromatography. Curr Protein Pept Sci 2018; 20:34-39. [PMID: 29065832 DOI: 10.2174/1389203718666171024121529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/25/2017] [Accepted: 09/09/2017] [Indexed: 11/22/2022]
Abstract
Previously, we have reviewed in this journal (Arakawa, T., Kita, Y., Curr. Protein Pept. Sci., 15, 608-620, 2014) the interaction of arginine with proteins and various applications of this solvent additive in the area of protein formulations and downstream processes. In this special issue, we expand the concept of protein-solvent interaction into the analysis of the effects of solvent additives on various column chromatography, including mixed-mode chromatography. Earlier in our research, we have studied the interactions of such a variety of solvent additives as sugars, salts, amino acids, polymers and organic solvents with a variety of proteins, which resulted in mechanistic understanding on their protein stabilization and precipitation effects, the latter known as Hofmeister series. While such a study was then a pure academic research, rapid development of genetic engineering technologies and resultant biotechnologies made it a valuable knowledge in fully utilizing solvent additives in manipulation of protein solution, including column chromatography.
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Affiliation(s)
- Tsutomu Arakawa
- Alliance Protein Laboratories, A Division of KBI Biopharma, 6042 Cornerstone Court West, San Diego, CA 92121, United States
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16
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Arakawa T, Gagnon P. Excluded Cosolvent in Chromatography. J Pharm Sci 2018; 107:2297-2305. [DOI: 10.1016/j.xphs.2018.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/02/2018] [Indexed: 10/14/2022]
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17
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Wang Z, Lu HP. Single-Molecule Spectroscopy Study of Crowding-Induced Protein Spontaneous Denature and Crowding-Perturbed Unfolding–Folding Conformational Fluctuation Dynamics. J Phys Chem B 2018; 122:6724-6732. [DOI: 10.1021/acs.jpcb.8b03119] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Zijiang Wang
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - H. Peter Lu
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
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18
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Kim J, Krebs MRH, Trout BL. Retracted: Molecular characterization of excipients' preferential interactions with therapeutic monoclonal antibodies. J Pharm Pharmacol 2018; 70:289-304. [PMID: 28776673 DOI: 10.1111/jphp.12787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 06/18/2017] [Indexed: 10/19/2022]
Abstract
Retraction: Molecular characterization of excipients' preferential interactions with therapeutic monoclonal antibodies by Jehoon Kim, Mark R. H. Krebs and Bernhardt L. Trout The above article from the Journal of Pharmacy and Pharmacology, first published online on 4 August 2017 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the authors, the journal Editor-in-Chief, Professor David Jones, and John Wiley & Sons Ltd. The authors discovered that the analysis of simulations was faulty making the data incorrect. Reference Kim J et al. Molecular characterization of excipients' preferential interactions with therapeutic monoclonal antibodies. J Pharm Pharmacol 2017. https://doi.org/10.1111/jphp.12787.
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Affiliation(s)
- Jehoon Kim
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mark R H Krebs
- Protein Pharmaceutical Development, Biogen, Cambridge, MA, USA
| | - Bernhardt L Trout
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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19
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Bruździak P, Panuszko A, Kaczkowska E, Piotrowski B, Daghir A, Demkowicz S, Stangret J. Taurine as a water structure breaker and protein stabilizer. Amino Acids 2018; 50:125-140. [PMID: 29043510 PMCID: PMC5762795 DOI: 10.1007/s00726-017-2499-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/26/2017] [Indexed: 12/24/2022]
Abstract
The enhancing effect on the water structure has been confirmed for most of the osmolytes exhibiting both stabilizing and destabilizing properties in regard to proteins. The presented work concerns osmolytes, which should be classified as "structure breaking" solutes: taurine and N,N,N-trimethyltaurine (TMT). Here, we combine FTIR spectroscopy, DSC calorimetry and DFT calculations to gain an insight into the interactions between osmolytes and two proteins: lysozyme and ubiquitin. Despite high structural similarity, both osmolytes exert different influence on protein stability: taurine is a stabilizer, TMT is a denaturant. We show also that taurine amino group interacts directly with the side chains of proteins, whereas TMT does not interact with proteins at all. Although two solutes weaken on average the structure of the surrounding water, their hydration spheres are different. Taurine is surrounded by two populations of water molecules: bonded with weak H-bonds around sulfonate group, and strongly bonded around amino group. The strong hydrogen-bonded network of water molecules around the amino group of taurine further improves properties of enhanced protein hydration sphere and stabilizes the native protein form. Direct interactions of this group with surface side chains provide a proper orientation of taurine and prevents the [Formula: see text] group from negative influence. The weakened [Formula: see text] hydration sphere of TMT breaks up the hydrogen-bonded network of water around the protein and destabilizes it. However, TMT at low concentration stabilize both proteins to a small extent. This effect can be attributed to an actual osmophobic effect which is overcome if the concentration increases.
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Affiliation(s)
- P Bruździak
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland.
| | - A Panuszko
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - E Kaczkowska
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - B Piotrowski
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - A Daghir
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - S Demkowicz
- Department of Organic Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - J Stangret
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland
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20
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Braun MK, Grimaldo M, Roosen-Runge F, Hoffmann I, Czakkel O, Sztucki M, Zhang F, Schreiber F, Seydel T. Crowding-Controlled Cluster Size in Concentrated Aqueous Protein Solutions: Structure, Self- and Collective Diffusion. J Phys Chem Lett 2017; 8:2590-2596. [PMID: 28525282 DOI: 10.1021/acs.jpclett.7b00658] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We investigate the concentration-controlled formation of clusters in β-lactoglobulin (BLG) protein solutions combining structural and dynamical scattering techniques. The static structure factor from small-angle X-ray scattering as well as de-Gennes narrowing in the nanosecond diffusion function D(q) from neutron spin echo spectroscopy support a picture of cluster formation. Using neutron backscattering spectroscopy, a monotonous increase of the average hydrodynamic cluster radius is monitored over a broad protein concentration range, corresponding to oligomeric structures of BLG ranging from the native dimers up to roughly four dimers. The results suggest that BLG forms compact clusters that are static on the observation time scale of several nanoseconds. The presented analysis provides a general framework to access the structure and dynamics of macromolecular assemblies in solution.
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Affiliation(s)
- Michal K Braun
- Institut für Angewandte Physik, Universität Tübingen , Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Marco Grimaldo
- Institut für Angewandte Physik, Universität Tübingen , Auf der Morgenstelle 10, 72076 Tübingen, Germany
- Institut Laue-Langevin , 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Felix Roosen-Runge
- Institut Laue-Langevin , 71 Avenue des Martyrs, 38000 Grenoble, France
- Division of Physical Chemistry, Department of Chemistry, Lund University , Naturvetarvägen 14, 221 00 Lund, Sweden
| | - Ingo Hoffmann
- Institut Laue-Langevin , 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Orsolya Czakkel
- Institut Laue-Langevin , 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Michael Sztucki
- ESRF - The European Synchrotron , 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen , Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen , Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Tilo Seydel
- Institut Laue-Langevin , 71 Avenue des Martyrs, 38000 Grenoble, France
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21
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Huang PY, Gao JY, Song CY, Hong JL. Multiple-responsive ionic complex luminogen of quinine and camphorsulfonic acid with aggregation-induced emission. RSC Adv 2016. [DOI: 10.1039/c6ra00603e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Bulky camphorsulfonic acid (CSA) was used to complex with quinine (Qu) to impose restricted intramolecular rotation (RIR) required for aggregation-induced emission (AIE) properties.
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Affiliation(s)
- Pei-Yi Huang
- Department of Materials and Optoelectronic Science
- National Sun Yat-sen University
- Kaohsiung 80424
- Republic of China
| | - Jhen-Yan Gao
- Department of Materials and Optoelectronic Science
- National Sun Yat-sen University
- Kaohsiung 80424
- Republic of China
| | - Cheng-Yu Song
- Department of Materials and Optoelectronic Science
- National Sun Yat-sen University
- Kaohsiung 80424
- Republic of China
| | - Jin-Long Hong
- Department of Materials and Optoelectronic Science
- National Sun Yat-sen University
- Kaohsiung 80424
- Republic of China
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22
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Beg I, Minton AP, Hassan I, Islam A, Ahmad F. Thermal Stabilization of Proteins by Mono- and Oligosaccharides: Measurement and Analysis in the Context of an Excluded Volume Model. Biochemistry 2015; 54:3594-603. [PMID: 26000826 DOI: 10.1021/acs.biochem.5b00415] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reversible thermal denaturation of apo α-lactalbumin and lysozyme was monitored via measurement of changes in absorbance and ellipticity in the presence of varying concentrations of seven mono- and oligosaccharides: glucose, galactose, fructose, sucrose, trehalose, raffinose, and stachyose. The temperature dependence of the unfolding curves was quantitatively accounted for by a two-state model, according to which the free energy of unfolding is increased by an amount that is independent of temperature and depends linearly upon the concentration of added saccharide. The increment of added unfolding free energy per mole of added saccharide was found to depend approximately linearly upon the extent of oligomerization of the saccharide. The relative strength of stabilization of different saccharide oligomers could be accounted for by a simplified statistical-thermodynamic model attributing the stabilization effect to volume exclusion deriving from steric repulsion between protein and saccharide molecules.
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Affiliation(s)
- Ilyas Beg
- †Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Allen P Minton
- ‡National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Imtaiyaz Hassan
- †Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Asimul Islam
- †Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Faizan Ahmad
- †Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
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23
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Platts L, Falconer RJ. Controlling protein stability: Mechanisms revealed using formulations of arginine, glycine and guanidinium HCl with three globular proteins. Int J Pharm 2015; 486:131-5. [DOI: 10.1016/j.ijpharm.2015.03.051] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 03/23/2015] [Accepted: 03/25/2015] [Indexed: 10/23/2022]
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24
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Abstract
The partial specific (or molar) volume, expansibility, and compressibility of a protein are fundamental thermodynamic quantities for characterizing its structure in solution. We review the definitions, measurements, and implications of these volumetric quantities in relation to protein structural biology. The partial specific volumes under constant molality (isomolal) and chemical potential (isopotential) conditions of the cosolvent (multicomponent systems) are explained in terms of preferential solvent interactions relevant to the solubility and stability of proteins. The partial expansibility is briefly discussed in terms of the effects of temperature on protein-solvent interactions (hydration) and internal packing defects (cavities). We discuss the compressibility-structure-function relationships of proteins based on analyses of the correlations between the partial adiabatic compressibilities and the structures or functions of various globular proteins (including mutants), focusing on the roles of the internal cavities in structural fluctuations. The volume and compressibility changes associated with various conformational transitions are also discussed in terms of the changes in hydration and cavities in order to elucidate the nonnative structures and the transition mechanisms, especially those associated with pressure denaturation.
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25
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Saha S, Deep S. Switch in the Aggregation Pathway of Bovine Serum Albumin Mediated by Electrostatic Interactions. J Phys Chem B 2014; 118:9155-66. [DOI: 10.1021/jp502435f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shivnetra Saha
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz-Khas, New Delhi 110016, India
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz-Khas, New Delhi 110016, India
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26
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Sashi P, Yasin UM, Balasubramanian H, Sree MU, Ramakrishna D, Bhuyan AK. Preferential water exclusion in protein unfolding. J Phys Chem B 2014; 118:717-23. [PMID: 24354363 DOI: 10.1021/jp4111103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Association of water with protein plays a central role in the latter's folding, structure acquisition, ligand binding, catalytic reactivity, oligomerization, and crystallization. Because these phenomena are also influenced by the net charge content on the protein, the present study examines the association of water with cytochrome c held at different pH values so as to allow its side chains to ionize to variable extents. Equilibrium unfolding of differently charged cytochrome c molecules in water-methanol binary mixtures, where the alcohol acts as the cosolvent denaturant, was used to quantify the preferential exclusion of water during the unfolding transition. The extent of exclusion was found to be related to the net-charge-dependent molecular expansion of the protein in an alcohol-free aqueous medium. The degree of water exclusion was also found to be linearly related to the observed rate of protein unfolding, where the net charge contents of the initial and final states are the same. The results suggest that side-chain ionization, molecular expansion due to charge repulsion, and hence the loss of tertiary contacts lead to additional water-protein association. Protein unfolding rates appear to be linearly correlated with the effective number of water molecules excluded across the end states of unfolding equilibria.
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Affiliation(s)
- Pulikallu Sashi
- School of Chemistry University of Hyderabad , Hyderabad 500 046, India
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27
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Tripathy J, Mueller JJ, Shepherd NC, Beck WF. Dynamic solvation and coupling of the hydration shell of Zn(II)-substituted cytochrome c in the presence of guanidinium ions. J Phys Chem B 2013; 117:14589-98. [PMID: 24237324 DOI: 10.1021/jp404554t] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The fluorescence Stokes shift (FSS) response of Zn(II)-substituted cytochrome c (ZnCytc) is transformed from a monotonic red-shifting response in water to a bidirectional response with much slower time constants in the presence of low concentrations of guanidinium (Gdm(+)) ions. The FSS response in water observed over the 100 ps to 10 ns range has two exponential components with time constants of 135 ps and 1.6 ns that account for a total shift of 30 cm(-1), about one-half of the solvation reorganization energy. In contrast, in the presence of only 0.25 M Gdm(+), the FSS response initially shifts 21 cm(-1) to the blue with a 820 ps time constant and then shifts 60 cm(-1) back to the red with a 3.5 ns time constant. The effect of Gdm(+) on the FSS response effectively saturates at 1.0 M, well below the 1.75 M midpoint of the two-state unfolding transition. These results establish that the FSS response in ZnCytc includes a significant contribution from the surrounding hydration shell, which assumes a perturbed hydrogen-bonding network owing to the binding of Gdm(+) ions to the protein surface. The blue-shifting part of the FSS response arises from a light-induced conformational change that expands the protein- and solvent-derived cavity around the excited-state Zn(II) porphyrin. This non-polar part of the solvation response is enhanced in the presence of Gdm(+) because the protein/solvent surroundings of the Zn(II) porphyrin are effectively more flexible than in water. The enhanced flexibility in the presence of Gdm(+) increases the amplitudes and accordingly lengthens the correlation time scales for the protein and hydration-shell fluctuations that contribute to the FSS response.
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Affiliation(s)
- Jagnyaseni Tripathy
- Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
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28
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Moghaddamnia MH, Saboury AA, Hakimelahi GH, Moosavi-Moovahedi AA. Denaturation of Adenosine Deaminase with Urea and Guanidine Hydrochloride. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.199700063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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29
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Sukenik S, Sapir L, Gilman-Politi R, Harries D. Diversity in the mechanisms of cosolute action on biomolecular processes. Faraday Discuss 2013; 160:225-37; discussion 311-27. [PMID: 23795502 DOI: 10.1039/c2fd20101a] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Numerous cellular cosolutes significantly impact the way that proteins and other biomacromolecules act and interact. We have followed the thermodynamic effect of several cosolute classes, including polymers, cellular osmolytes, and inorganic salts, on the stability of biomolecular folding and complexation. By comparing changes in free energy, enthalpy, and entropy upon cosolutes addition for these processes, we identify several thermodynamically distinct mechanisms. Surprisingly, even while many cosolutes display similar scaling of the change in stabilizing free energy with their concentration, a breakdown of this free energy into enthalpic and entropic contributions distinguishes different families of cosolutes. We discuss how these "thermodynamic fingerprints" can direct towards possible underlying mechanisms that govern the cosolute effect.
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Affiliation(s)
- Shahar Sukenik
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem, Israel
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30
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Fagan JA, Zheng M, Rastogi V, Simpson JR, Khripin CY, Silvera Batista CA, Hight Walker AR. Analyzing surfactant structures on length and chirality resolved (6,5) single-wall carbon nanotubes by analytical ultracentrifugation. ACS NANO 2013; 7:3373-87. [PMID: 23530719 DOI: 10.1021/nn4002165] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The structure and density of the bound interfacial surfactant layer and associated hydration shell were investigated using analytical ultracentrifugation for length and chirality purified (6,5) single-wall carbon nanotubes (SWCNTs) in three different bile salt surfactant solutions. The differences in the chemical structures of the surfactants significantly affect the size and density of the bound surfactant layers. As probed by exchange of a common parent nanotube population into sodium deoxycholate, sodium cholate, or sodium taurodeoxycholate solutions, the anhydrous density of the nanotubes was least for the sodium taurodeoxycholate surfactant, and the absolute sedimentation velocities greatest for the sodium cholate and sodium taurodeoxycholate surfactants. These results suggest that the thickest interfacial layer is formed by the deoxycholate, and that the taurodeoxycholate packs more densely than either sodium cholate or deoxycholate. These structural differences correlate well to an observed 25% increase in fluorescence intensity relative to the cholate surfactant for deoxycholate and taurodeoxycholate dispersed SWCNTs displaying equivalent absorbance spectra. Separate sedimentation velocity experiments including the density modifying agent iodixanol were used to establish the buoyant density of the (6,5) SWCNT in each of the bile salt surfactants; from the difference in the buoyant and anhydrous densities, the largest hydrated diameter is observed for sodium deoxycholate. Understanding the effects of dispersant choice and the methodology for measurement of the interfacial density and hydrated diameter is critical for rationally advancing separation strategies and applications of nanotubes.
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Affiliation(s)
- Jeffrey A Fagan
- National Institute of Standards and Technology, Materials Science and Engineering Division, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States.
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31
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Kinetic Analysis of Guanidine Hydrochloride Inactivation of β-Galactosidase in the Presence of Galactose. Enzyme Res 2012; 2012:173831. [PMID: 23008759 PMCID: PMC3449116 DOI: 10.1155/2012/173831] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Revised: 07/28/2012] [Accepted: 07/29/2012] [Indexed: 12/03/2022] Open
Abstract
Inactivation of purified β-Galactosidase was done with GdnHCl in the absence and presence of varying [galactose] at 50°C and at pH 4.5. Lineweaver-Burk plots of initial velocity data, in the presence and absence of guanidine hydrochloride (GdnHCl) and galactose, were used to determine the relevant Km and Vmax values, with p-nitrophenyl β-D-galactopyranoside (pNPG) as substrate, S. Plots of ln([P]∞ − [P]t) against time in the presence of GdnHCl yielded the inactivation rate constant, A. Plots of A versus [S] at different galactose concentrations were straight lines that became increasingly less steep as the [galactose] increased, showing that A was dependent on [S]. Slopes and intercepts of the 1/[P]∞ versus 1/[S] yielded k+0
and k'+0, the microscopic rate constants for the free enzyme and the enzyme-substrate complex, respectively. Plots of k+0
and k'+0 versus [galactose] showed that galactose protected the free enzyme as well as the enzyme-substrate complex (only at the lowest and highest [galactose]) against GdnHCl inactivation. In the absence of galactose, GdnHCl exhibited some degree of non-competitive inhibition. In the presence of GdnHCl, galactose exhibited competitive inhibition at the lower [galactose] of 5 mM which changed to non-competitive as the [galactose] increased. The implications of our findings are further discussed.
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32
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Refolding Technology for scFv Using a New Detergent, N-Lauroyl-L-glutamate and Arginine. Antibodies (Basel) 2012. [DOI: 10.3390/antib1020215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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33
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Jones EM, Dubey M, Camp PJ, Vernon BC, Biernat J, Mandelkow E, Majewski J, Chi EY. Interaction of tau protein with model lipid membranes induces tau structural compaction and membrane disruption. Biochemistry 2012; 51:2539-50. [PMID: 22401494 DOI: 10.1021/bi201857v] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The misfolding and aggregation of the intrinsically disordered, microtubule-associated tau protein into neurofibrillary tangles is implicated in the pathogenesis of Alzheimer's disease. However, the mechanisms of tau aggregation and toxicity remain unknown. Recent work has shown that anionic lipid membranes can induce tau aggregation and that membrane permeabilization may serve as a pathway by which protein aggregates exert toxicity, suggesting that the plasma membrane may play dual roles in tau pathology. This prompted our investigation to assess tau's propensity to interact with membranes and to elucidate the mutually disruptive structural perturbations the interactions induce in both tau and the membrane. We show that although highly charged and soluble, the full-length tau (hTau40) is also highly surface active, selectively inserts into anionic DMPG lipid monolayers and induces membrane morphological changes. To resolve molecular-scale structural details of hTau40 associated with lipid membranes, X-ray and neutron scattering techniques are utilized. X-ray reflectivity indicates hTau40s presence underneath a DMPG monolayer and penetration into the lipid headgroups and tailgroups, whereas grazing incidence X-ray diffraction shows that hTau40 insertion disrupts lipid packing. Moreover, both air/water and DMPG lipid membrane interfaces induce the disordered hTau40 to partially adopt a more compact conformation with density similar to that of a folded protein. Neutron reflectivity shows that tau completely disrupts supported DMPG bilayers while leaving the neutral DPPC bilayer intact. Our results show that hTau40s strong interaction with anionic lipids induces tau structural compaction and membrane disruption, suggesting possible membrane-based mechanisms of tau aggregation and toxicity in neurodegenerative diseases.
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Affiliation(s)
- Emmalee M Jones
- Department of Chemical and Nuclear Engineering, Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States
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34
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Li W, Mu Y. Dissociation of hydrophobic and charged nano particles in aqueous guanidinium chloride and urea solutions: a molecular dynamics study. NANOSCALE 2012; 4:1154-1159. [PMID: 22105862 DOI: 10.1039/c1nr11108f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
It has been a long history that urea and guanidinium chloride (GdmCl) are used as agents for denaturing proteins. The underlying mechanism has been extensively studied in the past several decades. However, the question regarding why GdmCl is much stronger than urea has seldom been touched. Here, through molecular dynamics simulations, we show that a 4 M GdmCl solution is more able than 7 M urea solution to dissociate both hydrophobic and charged nano-particles (NP). Both urea and GdmCl affect the NPs' aggregation through direct binding to the NP surface. The advantages of GdmCl originate from the net charge of bound guanidinium ions which can generate a local positively charged environment around hydrophobic and negatively charged NPs. This effective coating can introduce Coulombic repulsion between all the NPs. Urea shows certain ability to dissociate hydrophobic NPs. However, in the case of charged NPs, urea molecules located between two opposite-charged NPs will form ordered hydrogen bonds, acting like "glue" which prevents separation of the NPs. Although urea can form hydrogen bonds with either hydrophilic amino acids or the protein backbone, which are believed to contribute to protein denaturation, our findings strongly suggest that this property does not always contribute positively to urea's denaturation power.
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Affiliation(s)
- Weifeng Li
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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35
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Yoshikawa H, Hirano A, Arakawa T, Shiraki K. Mechanistic insights into protein precipitation by alcohol. Int J Biol Macromol 2011; 50:865-71. [PMID: 22115717 DOI: 10.1016/j.ijbiomac.2011.11.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Revised: 11/08/2011] [Accepted: 11/08/2011] [Indexed: 10/15/2022]
Abstract
Ethanol is used to precipitate proteins during various processes, including purification and crystallization. To elucidate the mechanism of protein precipitation by alcohol, we have investigated the solubility and structural changes of protein over a wide range of alcohol concentrations. Conformation of hen egg-white lysozyme was changed from native to α-helical rich structure in the presence of ethanol at concentrations above 60%. The solubility of lysozyme was reduced with increasing ethanol concentration, although gel formation at ethanol concentrations between 60% and 75% prevented accurate solubility measurements. SH-modified lysozyme showed largely unfolded structure in water and α-helical structure in the presence of ethanol. More importantly, solubility of the chemically modified lysozyme molecules decreased with increasing ethanol concentration. There is no indication of increased solubility upon unfolding of the lysozyme molecules by ethanol, indicating that any favorable interaction of ethanol with the hydrophobic side chains, if indeed occuring, is offset by the unfavorable interaction of ethanol with the hydrophilic side chains and peptide bonds.
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Affiliation(s)
- Hiroki Yoshikawa
- Institute of Applied Physics, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
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36
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Wernersson E, Heyda J, Vazdar M, Lund M, Mason PE, Jungwirth P. Orientational Dependence of the Affinity of Guanidinium Ions to the Water Surface. J Phys Chem B 2011; 115:12521-6. [PMID: 21985190 DOI: 10.1021/jp207499s] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Erik Wernersson
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Jan Heyda
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Mario Vazdar
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Division of Organic Chemistry and Biochemistry, Rudjer Bošković Institute, P.O. Box 180, HR-10002 Zagreb, Croatia
| | - Mikael Lund
- Department of Theoretical Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Philip E. Mason
- Department of Food Science, Stocking Hall, Cornell University, Ithaca, New York 14853, United States
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
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37
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Kamerzell TJ, Esfandiary R, Joshi SB, Middaugh CR, Volkin DB. Protein-excipient interactions: mechanisms and biophysical characterization applied to protein formulation development. Adv Drug Deliv Rev 2011; 63:1118-59. [PMID: 21855584 DOI: 10.1016/j.addr.2011.07.006] [Citation(s) in RCA: 350] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 07/19/2011] [Accepted: 07/26/2011] [Indexed: 12/18/2022]
Abstract
The purpose of this review is to demonstrate the critical importance of understanding protein-excipient interactions as a key step in the rational design of formulations to stabilize and deliver protein-based therapeutic drugs and vaccines. Biophysical methods used to examine various molecular interactions between solutes and protein molecules are discussed with an emphasis on applications to pharmaceutical excipients in terms of their effects on protein stability. Key mechanisms of protein-excipient interactions such as electrostatic and cation-pi interactions, preferential hydration, dispersive forces, and hydrogen bonding are presented in the context of different physical states of the formulation such as frozen liquids, solutions, gels, freeze-dried solids and interfacial phenomenon. An overview of the different classes of pharmaceutical excipients used to formulate and stabilize protein therapeutic drugs is also presented along with the rationale for use in different dosage forms including practical pharmaceutical considerations. The utility of high throughput analytical methodologies to examine protein-excipient interactions is presented in terms of expanding formulation design space and accelerating experimental timelines.
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Affiliation(s)
- Tim J Kamerzell
- Cardiovascular Research Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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38
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Interactions of formulation excipients with proteins in solution and in the dried state. Adv Drug Deliv Rev 2011; 63:1053-73. [PMID: 21756953 DOI: 10.1016/j.addr.2011.06.011] [Citation(s) in RCA: 265] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 06/18/2011] [Accepted: 06/23/2011] [Indexed: 12/12/2022]
Abstract
A variety of excipients are used to stabilize proteins, suppress protein aggregation, reduce surface adsorption, or to simply provide physiological osmolality. The stabilizers encompass a wide variety of molecules including sugars, salts, polymers, surfactants, and amino acids, in particular arginine. The effects of these excipients on protein stability in solution are mainly caused by their interaction with the protein and the container surface, and most importantly with water. Some excipients stabilize proteins in solution by direct binding, while others use a number of fundamentally different mechanisms that involve indirect interactions. In the dry state, any effects that the excipients confer to proteins through their interactions with water are irrelevant, as water is no longer present. Rather, the excipients stabilize proteins through direct binding and their effects on the physical properties of the dried powder. This review will describe a number of mechanisms by which the excipients interact with proteins in solution and with various interfaces, and their effects on the physical properties of the dried protein structure, and explain how the various interaction forces are related to their observed effects on protein stability.
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39
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Abstract
Macromolecular crowding in biological media is an essential factor for cellular function. The interplay of intermolecular interactions at multiple time and length scales governs a fine-tuned system of reaction and transport processes, including particularly protein diffusion as a limiting or driving factor. Using quasielastic neutron backscattering, we probe the protein self-diffusion in crowded aqueous solutions of bovine serum albumin on nanosecond time and nanometer length scales employing the same protein as crowding agent. The measured diffusion coefficient D(ϕ) strongly decreases with increasing protein volume fraction ϕ explored within 7% ≤ ϕ ≤ 30%. With an ellipsoidal protein model and an analytical framework involving colloid diffusion theory, we separate the rotational D(r)(ϕ) and translational D(t)(ϕ) contributions to D(ϕ). The resulting D(t)(ϕ) is described by short-time self-diffusion of effective spheres. Protein self-diffusion at biological volume fractions is found to be slowed down to 20% of the dilute limit solely due to hydrodynamic interactions.
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40
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Fisicaro E, Compari C, Braibanti A. Hydrophobic hydration processes thermal and chemical denaturation of proteins. Biophys Chem 2011; 156:51-67. [PMID: 21482019 DOI: 10.1016/j.bpc.2011.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 02/21/2011] [Accepted: 02/21/2011] [Indexed: 10/18/2022]
Abstract
The hydrophobic hydration processes have been analysed under the light of a mixture model of water that is assumed to be composed by clusters (W(5))(I), clusters (W(4))(II) and free water molecules W(III). The hydrophobic hydration processes can be subdivided into two Classes A and B. In the processes of Class A, the transformation A(-ξ(w)W(I)→ξ(w)W(II)+ξ(w)W(III)+cavity) takes place, with expulsion from the bulk of ξ(w) water molecules W(III), whereas in the processes of Class B the opposite transformation B(-ξ(w)W(III)-ξ(w)W(II)→ξ(w)W(I)-cavity) takes place, with condensation into the bulk of ξ(w) water molecules W(III). The thermal equivalent dilution (TED) principle is exploited to determine the number ξ(w). The denaturation (unfolding) process belongs to Class A whereas folding (or renaturation) belongs to Class B. The enthalpy ΔH(den) and entropy ΔS(den) functions can be disaggregated in thermal and motive components, ΔH(den)=ΔH(therm)+ΔH(mot), and ΔS(den)=ΔS(therm)+ΔS(mot), respectively. The terms ΔH(therm) and ΔS(therm) are related to phase change of water molecules W(III), and give no contribution to free energy (ΔG(therm)=0). The motive functions refer to the process of cavity formation (Class A) or cavity reduction (Class B), respectively and are the only contributors to free energy ΔG(mot). The folded native protein is thermodynamically favoured (ΔG(fold)≡ΔG(mot)<0) because of the outstanding contribution of the positive entropy term for cavity reduction, ΔS(red)≫0. The native protein can be brought to a stable denatured state (ΔG(den)≡ΔG(mot)<0) by coupled reactions. Processes of protonation coupled to denaturation have been identified. In thermal denaturation by calorimetry, however, is the heat gradually supplied to the system that yields a change of phase of water W(III), with creation of cavity and negative entropy production, ΔS(for)≪0. The negative entropy change reduces and at last neutralises the positive entropy of folding. In molecular terms, this means the gradual disruption by cavity formation of the entropy-driven hydrophobic bonds that had been keeping the chains folded in the native protein. The action of the chemical denaturants is similar to that of heat, by modulating the equilibrium between W(I), W(II), and W(III) toward cavity formation and negative entropy production. The salting-in effect produced by denaturants has been recognised as a hydrophobic hydration process belonging to Class A with cavity formation, whereas the salting-out effect produced by stabilisers belongs to Class B with cavity reduction. Some algorithms of denaturation thermodynamics are presented in the Appendices.
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Affiliation(s)
- E Fisicaro
- Department of Pharmacological, Biological and Applied Chem. Sciences, Physical Chemistry Section, University of Parma, Italy.
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41
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Sirotkin VA, Winter R. Volume Changes Associated with Guanidine Hydrochloride, Temperature, and Ethanol Induced Unfolding of Lysozyme. J Phys Chem B 2010; 114:16881-6. [DOI: 10.1021/jp105627w] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vladimir A. Sirotkin
- A. M. Butlerov Institute of Chemistry, Kazan Federal University, Kremlevskaya Str., 18, 420008, Kazan, Russia, and Faculty of Chemistry, Physical Chemistry I, Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Roland Winter
- A. M. Butlerov Institute of Chemistry, Kazan Federal University, Kremlevskaya Str., 18, 420008, Kazan, Russia, and Faculty of Chemistry, Physical Chemistry I, Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
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42
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Held C, Neuhaus T, Sadowski G. Compatible solutes: Thermodynamic properties and biological impact of ectoines and prolines. Biophys Chem 2010; 152:28-39. [DOI: 10.1016/j.bpc.2010.07.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Revised: 07/26/2010] [Accepted: 07/27/2010] [Indexed: 10/19/2022]
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43
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Arakawa T, Ejima D, Li T, Philo JS. The critical role of mobile phase composition in size exclusion chromatography of protein pharmaceuticals. J Pharm Sci 2010; 99:1674-92. [PMID: 19894271 DOI: 10.1002/jps.21974] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Size exclusion chromatography (SEC) is the most widely used method for aggregation analysis of pharmaceutical proteins. However SEC analysis has a number of limitations, and one of the most important ones is protein adsorption to the resin. This problem is particularly severe when using new columns, and often column preconditioning protocols are required. This review focuses on the role that addition of various cosolvents to the mobile phase plays in suppressing that protein adsorption. Cosolvents such as salt, amino acids, and organic solvents are often used for this purpose. Because the protein interaction with the resin surface is highly heterogeneous, different cosolvents affect the protein adsorption differently. We will summarize the various effects of cosolvents on protein adsorption and retention and describe the mechanism of the cosolvent effects.
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Affiliation(s)
- Tsutomu Arakawa
- Alliance Protein Laboratories, Thousand Oaks, California, USA.
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44
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Mason PE, Dempsey CE, Neilson GW, Kline SR, Brady JW. Preferential interactions of guanidinum ions with aromatic groups over aliphatic groups. J Am Chem Soc 2010; 131:16689-96. [PMID: 19874022 DOI: 10.1021/ja903478s] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Small angle neutron scattering (SANS) and molecular dynamics (MD) simulations were used to characterize the long-range structuring (aggregation) of aqueous solutions of isopropanol (IPA) and pyridine and the effect on structuring of guanidinium chloride (GdmCl). These solutes serve as highly soluble analogs of the nonpolar aliphatic (IPA) and aromatic (pyridine) side chains of proteins. SANS data showed that isopropanol and pyridine both form clusters in water resulting from interaction between nonpolar groups of the solutes, with pyridine aggregation producing longer-range structuring than isopropanol in 3 m solutions. Addition of GdmCl at 3 m concentration considerably reduced pyridine aggregation but had no effect on isopropanol aggregation. MD simulations of these solutions support the conclusion that long-range structuring involves hydrophobic solute interactions and that Gdm(+) interacts with the planar pyridine group to suppress pyridine-pyridine interactions in solution. Hydrophobic interactions involving the aliphatic groups of isopropanol were unaffected by GdmCl, indicating that the planar and weakly hydrated Gdm(+) cation cannot make productive interactions with the highly curved or "lumpy" aliphatic groups of this solute. These observations support the conclusion that the effects of Gdm(+) ions on protein-stabilizing interactions involving aromatic amino acid side chains make significant contributions to the denaturant activity of GdmCl, whereas interactions with the "lumpy" aliphatic side chains are likely to be less important.
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Affiliation(s)
- Philip E Mason
- Department of Food Science, Cornell University, Ithaca, New York 14853, USA
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45
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Devred F, Barbier P, Lafitte D, Landrieu I, Lippens G, Peyrot V. Microtubule and MAPs: thermodynamics of complex formation by AUC, ITC, fluorescence, and NMR. Methods Cell Biol 2010; 95:449-80. [PMID: 20466148 DOI: 10.1016/s0091-679x(10)95023-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Microtubules are implicated in many essential cellular processes such as architecture, cell division, and intracellular traffic, due to their dynamic instability. This dynamicity is tightly regulated by microtubule-associated proteins (MAPs), such as tau and stathmin. Despite extensive studies motivated by their central role in physiological functions and pathological role in neurodegenerative diseases and cancer, the precise mechanisms of tau and stathmin binding to tubulin and their consequences on microtubule stability are still not fully understood. One of the most crucial points missing is a quantitative thermodynamic description of their interaction with tubulin/microtubules and of the tubulin complexes formed upon these interactions. In this chapter, we will focus on the use of analytical ultracentrifugation, isothermal titration calorimetry, and nuclear magnetic resonance-three powerful and complementary techniques in the field of MAP-tubulin/microtubule interactions, in addition to the spectrometric techniques and co-sedimentation approach. We will present the limits of these techniques to study this particular interaction and precautions that need to be taken during MAPs preparation. Understanding the molecular mechanisms that govern MAPs action on microtubular network will not only shed new light on the role of this crucial family of protein in the biology of the cell, but also hopefully open new paths to increase the therapeutic efficiency of microtubule-targeting drugs in cancers therapies and neurodegeneratives diseases prevention.
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Affiliation(s)
- François Devred
- CRO2, U911 Inserm, Aix-Marseille Université, 27 Bd Jean Moulin, 13385 Marseille cedex 05, France
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46
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Alday PH, Correia JJ. Macromolecular interaction of halichondrin B analogues eribulin (E7389) and ER-076349 with tubulin by analytical ultracentrifugation. Biochemistry 2009; 48:7927-38. [PMID: 19586046 DOI: 10.1021/bi900776u] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Halichondrin B is an antimitotic drug that inhibits microtubule assembly. To understand the molecular details of its interaction with tubulin, we investigated the binding of two halichondrin B analogues, eribulin (previously, ER-086526, E7389) and ER-076349, to tubulin by quantitative analytical ultracentrifugation. Eribulin is currently undergoing phase III clinical trials for cancer; ER-076349 is a closely related analogue with C.35 hydroxyl instead of C.35 primary amine [Towle, M. J., et al. (2001) Cancer Res. 61, 1013]. Below the critical concentration for microtubule assembly and in the presence of GDP, tubulin undergoes weak self-association into short curved oligomers. Eribulin inhibits this oligomer formation 4-6-fold, while ER-076349 slightly stimulates oligomer formation by 2-fold. This is in contrast to vinblastine which strongly stimulates large spiral polymers by 1000-fold under these same conditions. Vinblastine-induced spiral formation is strongly inhibited by both eribulin and ER-076349. Colchicine binding to the intradimer interface has no significant effect on small oligomer formation or the inhibitory activity of eribulin on this process. These results suggest that halichondrin B analogues bind to the interdimer interface or to the beta-subunit alone, disrupt polymer stability, and compete with vinblastine-induced spiral formation. Stathmin is known to form a tight 1:2 complex with tubulin. Eribulin strongly inhibits formation of the 1:2 stathmin-tubulin complex (>3.3 kcal/mol), while ER-076349 weakens formation of the 1:2 complex by approximately 1.9 kcal/mol. These results suggest that eribulin is a global inhibitor of tubulin polymer formation, disrupting tubulin-tubulin contacts at the interdimer interface. ER-076349 also perturbs tubulin-tubulin contacts, but in a more polymer specific manner, reflecting adaptability of the interdimer interface to drug and polymer polymorphism. These results suggest halichondrin B analogues exhibit unique tubulin-based activities that may underlie the clinical utility of these compounds.
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Affiliation(s)
- P Holland Alday
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi 39216, USA
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47
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48
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Miyawaki O. Thermodynamic analysis of protein unfolding in aqueous solutions as a multisite reaction of protein with water and solute molecules. Biophys Chem 2009; 144:46-52. [DOI: 10.1016/j.bpc.2009.06.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 06/06/2009] [Accepted: 06/09/2009] [Indexed: 11/28/2022]
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49
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Gangadhara, Ramesh Kumar P, Prakash V. The Stabilizing Effects of Polyols and Sugars on Porcine Pancreatic Lipase. J AM OIL CHEM SOC 2009. [DOI: 10.1007/s11746-009-1408-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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50
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CHANDRA BSURESH, PRAKASH V, RAO MNARASINGA. Partial specific volume and interaction of glycinin with solvent components in urea and guanidine hydrochloride. ACTA ACUST UNITED AC 2009. [DOI: 10.1111/j.1399-3011.1986.tb01803.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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