1
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Ó'Fágáin C, Colliton K. Storage and Lyophilization of Pure Proteins. Methods Mol Biol 2023; 2699:421-475. [PMID: 37647008 DOI: 10.1007/978-1-0716-3362-5_19] [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] [Indexed: 09/01/2023]
Abstract
This chapter outlines empirical procedures for the storage of pure proteins with preservation of high levels of biological activity. It describes simple and workable means of preventing microbial contamination and proteolytic degradation and the use of various types of stabilizing additives. It sets out the principles of lyophilization (a complex process comprising freezing, primary drying, and secondary drying stages, otherwise known as freeze-drying). There follows a general procedure for the use of lyophilizer apparatus with emphasis on best practice and on pitfalls to avoid. The use of modulated differential scanning calorimetry to measure the glass transition temperature, a key parameter in the design and successful operation of lyophilization processes, is described. This chapter concludes with brief summaries of interesting recent work in the field.
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Affiliation(s)
- Ciarán Ó'Fágáin
- School of Biotechnology, Dublin City University, Dublin, Ireland.
| | - Keith Colliton
- Pfizer Ireland Pharmaceuticals, Grange Castle Business Park, Dublin, Ireland
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2
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Instability Challenges and Stabilization Strategies of Pharmaceutical Proteins. Pharmaceutics 2022; 14:pharmaceutics14112533. [PMID: 36432723 PMCID: PMC9699111 DOI: 10.3390/pharmaceutics14112533] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/13/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Maintaining the structure of protein and peptide drugs has become one of the most important goals of scientists in recent decades. Cold and thermal denaturation conditions, lyophilization and freeze drying, different pH conditions, concentrations, ionic strength, environmental agitation, the interaction between the surface of liquid and air as well as liquid and solid, and even the architectural structure of storage containers are among the factors that affect the stability of these therapeutic biomacromolecules. The use of genetic engineering, side-directed mutagenesis, fusion strategies, solvent engineering, the addition of various preservatives, surfactants, and additives are some of the solutions to overcome these problems. This article will discuss the types of stress that lead to instabilities of different proteins used in pharmaceutics including regulatory proteins, antibodies, and antibody-drug conjugates, and then all the methods for fighting these stresses will be reviewed. New and existing analytical methods that are used to detect the instabilities, mainly changes in their primary and higher order structures, are briefly summarized.
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3
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Chen Y, Mutukuri TT, Wilson NE, Zhou QT. Pharmaceutical protein solids: Drying technology, solid-state characterization and stability. Adv Drug Deliv Rev 2021; 172:211-233. [PMID: 33705880 PMCID: PMC8107147 DOI: 10.1016/j.addr.2021.02.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/18/2021] [Accepted: 02/22/2021] [Indexed: 01/30/2023]
Abstract
Despite the boom in biologics over the past decade, the intrinsic instability of these large molecules poses significant challenges to formulation development. Almost half of all pharmaceutical protein products are formulated in the solid form to preserve protein native structure and extend product shelf-life. In this review, both traditional and emerging drying techniques for producing protein solids will be discussed. During the drying process, various stresses can impact the stability of protein solids. However, understanding the impact of stress on protein product quality can be challenging due to the lack of reliable characterization techniques for biological solids. Both conventional and advanced characterization techniques are discussed including differential scanning calorimetry (DSC), solid-state Fourier transform infrared spectrometry (ssFTIR), solid-state fluorescence spectrometry, solid-state hydrogen deuterium exchange (ssHDX), solid-state nuclear magnetic resonance (ssNMR) and solid-state photolytic labeling (ssPL). Advanced characterization tools may offer mechanistic investigations into local structural changes and interactions at higher resolutions. The continuous exploration of new drying techniques, as well as a better understanding of the effects caused by different drying techniques in solid state, would advance the formulation development of biological products with superior quality.
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Affiliation(s)
- Yuan Chen
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47907, USA
| | - Tarun Tejasvi Mutukuri
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47907, USA
| | - Nathan E Wilson
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47907, USA
| | - Qi Tony Zhou
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47907, USA.
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4
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Abstract
Cells of the vast majority of organisms are subject to temperature, pressure, pH, ionic strength, and other stresses. We discuss these effects in the light of protein folding and protein interactions in vitro, in complex environments, in cells, and in vivo. Protein phase diagrams provide a way of organizing different structural ensembles that occur under stress and how one can move among ensembles. Experiments that perturb biomolecules in vitro or in cells by stressing them have revealed much about the underlying forces that are competing to control protein stability, folding, and function. Two phenomena that emerge and serve to broadly classify effects of the cellular environment are crowding (mainly due to repulsive forces) and sticking (mainly due to attractive forces). The interior of cells is closely balanced between these emergent effects, and stress can tip the balance one way or the other. The free energy scale involved is small but significant on the scale of the "on/off switches" that control signaling in cells or of protein-protein association with a favorable function such as increased enzyme processivity. Quantitative tools from biophysical chemistry will play an important role in elucidating the world of crowding and sticking under stress.
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Affiliation(s)
- Mayank Boob
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, United States
| | - Yuhan Wang
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, United States
| | - Martin Gruebele
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, United States
- Department of Chemistry, Department of Physics, Center for the Physics of Living Cells, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, United States
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5
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Röder K, Joseph JA, Husic BE, Wales DJ. Energy Landscapes for Proteins: From Single Funnels to Multifunctional Systems. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201800175] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Konstantin Röder
- Department of ChemistryUniversity of CambridgeLensfield Road CB2 1EW Cambridge UK
| | - Jerelle A. Joseph
- Department of ChemistryUniversity of CambridgeLensfield Road CB2 1EW Cambridge UK
| | - Brooke E. Husic
- Department of ChemistryUniversity of CambridgeLensfield Road CB2 1EW Cambridge UK
| | - David J. Wales
- Department of ChemistryUniversity of CambridgeLensfield Road CB2 1EW Cambridge UK
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6
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Mizukami T, Abe Y, Maki K. Evidence for a Shared Mechanism in the Formation of Urea-Induced Kinetic and Equilibrium Intermediates of Horse Apomyoglobin from Ultrarapid Mixing Experiments. PLoS One 2015; 10:e0134238. [PMID: 26244984 PMCID: PMC4526358 DOI: 10.1371/journal.pone.0134238] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 07/07/2015] [Indexed: 11/24/2022] Open
Abstract
In this study, the equivalence of the kinetic mechanisms of the formation of urea-induced kinetic folding intermediates and non-native equilibrium states was investigated in apomyoglobin. Despite having similar structural properties, equilibrium and kinetic intermediates accumulate under different conditions and via different mechanisms, and it remains unknown whether their formation involves shared or distinct kinetic mechanisms. To investigate the potential mechanisms of formation, the refolding and unfolding kinetics of horse apomyoglobin were measured by continuous- and stopped-flow fluorescence over a time range from approximately 100 μs to 10 s, along with equilibrium unfolding transitions, as a function of urea concentration at pH 6.0 and 8°C. The formation of a kinetic intermediate was observed over a wider range of urea concentrations (0–2.2 M) than the formation of the native state (0–1.6 M). Additionally, the kinetic intermediate remained populated as the predominant equilibrium state under conditions where the native and unfolded states were unstable (at ~0.7–2 M urea). A continuous shift from the kinetic to the equilibrium intermediate was observed as urea concentrations increased from 0 M to ~2 M, which indicates that these states share a common kinetic folding mechanism. This finding supports the conclusion that these intermediates are equivalent. Our results in turn suggest that the regions of the protein that resist denaturant perturbations form during the earlier stages of folding, which further supports the structural equivalence of transient and equilibrium intermediates. An additional folding intermediate accumulated within ~140 μs of refolding and an unfolding intermediate accumulated in <1 ms of unfolding. Finally, by using quantitative modeling, we showed that a five-state sequential scheme appropriately describes the folding mechanism of horse apomyoglobin.
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Affiliation(s)
- Takuya Mizukami
- Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Yukiko Abe
- Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Kosuke Maki
- Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
- * E-mail:
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7
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Sirovetz BJ, Schafer NP, Wolynes PG. Water Mediated Interactions and the Protein Folding Phase Diagram in the Temperature–Pressure Plane. J Phys Chem B 2015; 119:11416-27. [DOI: 10.1021/acs.jpcb.5b03828] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Brian J. Sirovetz
- Center
for Theoretical Biological Physics, Rice University, 6500 Main
Street, Houston, Texas 77030, United States
- Department
of Chemistry, Rice University, Space Science 201, Houston, Texas 77251, United States
| | - Nicholas P. Schafer
- Center
for Theoretical Biological Physics, Rice University, 6500 Main
Street, Houston, Texas 77030, United States
| | - Peter G. Wolynes
- Center
for Theoretical Biological Physics, Rice University, 6500 Main
Street, Houston, Texas 77030, United States
- Department
of Chemistry, Rice University, Space Science 201, Houston, Texas 77251, United States
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8
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Ono K, Ito M, Hirota S, Takada S. Dimer domain swapping versus monomer folding in apo-myoglobin studied by molecular simulations. Phys Chem Chem Phys 2015; 17:5006-13. [DOI: 10.1039/c4cp05203j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Using a coarse-grained symmetrized Go model, we performed a series of folding simulations of two apo-myoglobin molecules restrained at a high density, addressing competition of formation of a domain-swapped dimer with folding to two monomer structures.
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Affiliation(s)
- Koji Ono
- Graduate School of Science
- Kyoto University
- Sakyo Kyoto 606-8502
- Japan
| | - Mashiho Ito
- Graduate School of Science
- Kyoto University
- Sakyo Kyoto 606-8502
- Japan
| | - Shun Hirota
- Graduate School of Materials Science
- Nara Institute of Science and Technology
- Nara 630-0192
- Japan
| | - Shoji Takada
- Graduate School of Science
- Kyoto University
- Sakyo Kyoto 606-8502
- Japan
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9
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Goodman JS, Chao SH, Pogorelov TV, Gruebele M. Filling up the heme pocket stabilizes apomyoglobin and speeds up its folding. J Phys Chem B 2014; 118:6511-8. [PMID: 24456280 PMCID: PMC4065233 DOI: 10.1021/jp412459z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Wild type apomyoglobin folds in at
least two steps: the ABGH core
rapidly, followed much later by the heme-binding CDEF core. We hypothesize
that the evolved heme-binding function of the CDEF core frustrates
its folding: it has a smaller contact order and is no more complex
topologically than ABGH, and thus, it should be able to fold faster.
Therefore, filling up the empty heme cavity of apomyoglobin with larger,
hydrophobic side chains should significantly stabilize the protein
and increase its folding rate. Molecular dynamics simulations allowed
us to design four different mutants with bulkier side chains that
increase the native bias of the CDEF region. In vitro thermal denaturation shows that the mutations increase folding stability
and bring the protein closer to two-state behavior, as judged by the
difference of fluorescence- and circular dichroism-detected protein
stability. Millisecond stopped flow measurements of the mutants exhibit
refolding kinetics that are over 4 times faster than the wild type’s.
We propose that myoglobin-like proteins not evolved to bind heme are
equally stable, and find an example. Our results illustrate how evolution
for function can force proteins to adapt frustrated folding mechanisms,
despite having simple topologies.
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Affiliation(s)
- J S Goodman
- Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
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10
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Matysiak S, Debenedetti PG, Rossky PJ. Role of hydrophobic hydration in protein stability: a 3D water-explicit protein model exhibiting cold and heat denaturation. J Phys Chem B 2012; 116:8095-104. [PMID: 22725973 DOI: 10.1021/jp3039175] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigate the microscopic mechanism of cold and heat denaturation using a 3D lattice model of a hydrated protein in which water is represented explicitly. The water model, which incorporates directional bonding and tetrahedral geometry, captures many aspects of water thermodynamics and properly describes hydrophobic hydration around apolar solutes because the hydrogen bonding rules in the model were gleaned from off-lattice atomistic simulations of water around representative protein structures. By incorporating local chain stiffness in the protein model, a homopolymer can fold into a β-hairpin. It is shown that the homopolymer can be folded by either attractive interactions between the monomers or as a direct consequence of the entropic cost of forming interfacial hydrogen bonds in the solvent. However, cold denaturation is not observed if the collapse transition is induced by intramolecular attractions. We further find that it is the changes in hydrophobic hydration with decreasing temperature that drive cold unfolding and that the overall process is enthalpically driven, whereas heat denaturation is entropically driven.
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Affiliation(s)
- Silvina Matysiak
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States.
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11
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Kubelka J. Time-resolved methods in biophysics. 9. Laser temperature-jump methods for investigating biomolecular dynamics. Photochem Photobiol Sci 2009; 8:499-512. [DOI: 10.1039/b819929a] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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12
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Davidovic M, Mattea C, Qvist J, Halle B. Protein Cold Denaturation as Seen From the Solvent. J Am Chem Soc 2008; 131:1025-36. [DOI: 10.1021/ja8056419] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Monika Davidovic
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, SE-22100 Lund, Sweden
| | - Carlos Mattea
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, SE-22100 Lund, Sweden
| | - Johan Qvist
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, SE-22100 Lund, Sweden
| | - Bertil Halle
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, SE-22100 Lund, Sweden
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13
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Affiliation(s)
- Peter J Rossky
- Department of Chemistry and Biochemistry and Institute for Computational Engineering and Sciences, University of Texas, Austin, TX 78712, USA.
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14
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Dametto M, Cárdenas AE. Computer simulations of the refolding of sperm whale apomyoglobin from high-temperature denaturated state. J Phys Chem B 2008; 112:9501-6. [PMID: 18616314 DOI: 10.1021/jp804300w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The refolding mechanism of apomyoglobin (apoMb) subsequent to high-temperature unfolding has been examined using computer simulations with atomic level detail. The folding of this protein has been extensively studied experimentally, providing a large database of folding parameters which can be probed using simulations. In the present study, 4-folding trajectories of apoMb were computed starting from coiled structures. A crystal structure of sperm whale myoglobin taken from the Protein Data Bank was used to construct the final native conformation by removal of the heme group followed by energy optimization. The initial unfolded conformations were obtained from high-temperature molecular dynamics simulations. Room-temperature refolding trajectories at neutral pH were obtained using the stochastic difference equation in length algorithm. The folding trajectories were compared with experimental results and two previous molecular dynamics studies at low pH. In contrast to the previous simulations, an extended intermediate with large helical content was not observed. In the present study, a structural collapse occurs without formation of helices or native contacts. Once the protein structure is more compact (radius of gyration<18 A) secondary and tertiary structures appear. These results suggest that apoMb follows a different folding pathway after high-temperature denaturation.
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Affiliation(s)
- Mariangela Dametto
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA
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15
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Lopez CF, Darst RK, Rossky PJ. Mechanistic elements of protein cold denaturation. J Phys Chem B 2008; 112:5961-7. [PMID: 18181599 DOI: 10.1021/jp075928t] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Globular proteins undergo structural transitions to denatured states when sufficient thermodynamic state or chemical perturbations are introduced to their native environment. Cold denaturation is a somewhat counterintuitive phenomenon whereby proteins lose their compact folded structure as a result of a temperature drop. The currently accepted explanation for cold denaturation is based on an associated favorable change in the contact free energy between water and nonpolar groups at colder temperatures which would weaken the hydrophobic interaction and is thought to eventually allow polymer entropy to disrupt protein tertiary structure. In this paper we explore how this environmental perturbation leads to changes in the protein hydration and local motions in apomyoglobin. We do this by analyzing changes in protein hydration and protein motion from molecular dynamics simulation trajectories initially at 310 K, followed by a temperature drop to 278 K. We observe an increase in the number of solvent contacts around the protein and, in particular, distinctly around nonpolar atoms. Further analysis shows that the fluctuations of some protein atoms increase with decreasing temperature. This is accompanied by an observed increase in the isothermal compressibility of the protein, indicating an increase in the protein interior interstitial space. Closer inspection reveals that atoms with increased compressibility and larger-than-expected fluctuations are localized within the protein core regions. These results provide insight into a description of the mechanism of cold denaturation. That is, the lower temperature leads to solvent-induced packing defects at the protein surface, and this more favorable water-protein interaction in turn destabilizes the overall protein structure.
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Affiliation(s)
- Carlos F Lopez
- Center for Computational Molecular Sciences, Institute for Computational Engineering and Science, and Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712-1167, USA
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16
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Nakagawa K, Yamada Y, Fujiwara K, Ikeguchi M. Interactions responsible for secondary structure formation during folding of equine beta-lactoglobulin. J Mol Biol 2007; 367:1205-14. [PMID: 17306296 DOI: 10.1016/j.jmb.2007.01.053] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2006] [Revised: 12/09/2006] [Accepted: 01/22/2007] [Indexed: 10/23/2022]
Abstract
Equine beta-lactoglobulin forms a compact intermediate at an acidic pH (A state). It also forms an expanded and helical conformation at low temperatures (C state). The structure of a single disulfide mutant C66A/C160A is similar to the A state in the presence of salts, while it is similar to the C state at low anion concentrations. We have investigated the temperature-dependent change in the secondary structure using circular dichroism and proline scanning mutagenesis. At low anion concentrations, the helical content increased linearly as temperature decreased. In the presence of salts, the A state was cooperatively transformed into the C state at low temperatures. This suggests the importance of hydrophobic interactions for stabilizing the A state. Peptides encompassing native-like and non-native alpha-helices were synthesized to investigate the interactions responsible for helix formation in the A and C states. These did not form stable helices, indicating that not only the helices in the A state but also the helices in the C state are stabilized by long-range interactions. A longer fragment, CHIBL, which encompasses the structured region in the A and C states, showed a helical structure. Proline-substituted mutants of CHIBL showed CD spectral changes similar to the corresponding mutants of the full-length protein in the C state. Therefore, CHIBL has a structure similar to the corresponding region of the full-length protein in the C state. This result indicates that interactions responsible for helix formation in the C state reside in the sequence of CHIBL, and that the sequences outside CHIBL are essential for secondary structure formation in the A state.
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Affiliation(s)
- Kanako Nakagawa
- Department of Bioinformatics, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
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17
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Unfolding of apomyoglobin studied with two-dimensional correlations of tryptophan, 8-anilino-1-naphthalenesulfonate, and pyrene fluorescence. J Mol Struct 2006. [DOI: 10.1016/j.molstruc.2006.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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18
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Wang G, Gao Y, Geng ML. Analysis of heterogeneous fluorescence decays in proteins. Using fluorescence lifetime of 8-anilino-1-naphthalenesulfonate to probe apomyoglobin unfolding at equilibrium. Biochim Biophys Acta Gen Subj 2006; 1760:1125-37. [PMID: 16730413 DOI: 10.1016/j.bbagen.2006.02.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2005] [Revised: 02/03/2006] [Accepted: 02/22/2006] [Indexed: 10/24/2022]
Abstract
The solvatochromic fluorescent dye 8-anilino-1-naphthalenesulfonate (ANS) is one of the popular probes of protein folding. Folding kinetics is tracked with ANS fluorescence intensity, usually interpreted as a reflection of protein structure-the hydrophobicity of the binding environments. Such simplistic view overlooks the complicated nature of ANS-protein complexes: the fluorescence characteristics are convoluted results of the ground state populational distribution of the probe-protein complex, the structural changes in the protein and the excited state photophysics of the probe. Understanding of the interplay of these aspects is crucial in accurate interpretation of the protein dynamics. In this work, the fluorescence decay of ANS complexed with apomyoglobin at different conformations denatured by pH is modeled. The fluorescence decay of the ANS-apomyoglobin complex contains information on not only apomyoglobin structure but also molecular populational distributions. The challenge in modeling fluorescence decay profiles originates from the convolution of heterogeneous binding and excited-state relaxation of the fluorescent probe. We analyzed frequency-domain fluorescence lifetime data of ANS-apomyoglobin with both maximum entropy methods (MEM) and nonlinear least squares methods (NLLS). MEM recovers a model of two expanding-and-merging lifetime distributions for ANS-apomyoglobin in the equilibrium transition from the native (N) through an intermediate (I-1) to the acid-unfolded state U(A). At pH 6.5 and above, when apomyoglobin is mostly populated at the N-state, ANS-apomyoglobin emits a predominant long-lifetime fluorescence from a relaxed charge transfer state S(1,CT) of ANS, and a short-lifetime fluorescence that is mainly from a nascent excited-state S(1,np) of ANS stabilized by the strong ANS-apomyoglobin interaction. Lowering the pH diminishes the contribution from the S(1,np) state. Meanwhile, more protein molecules become populated at the U(A) state, which exhibits a short lifetime that is not distinguishable from the S(1,np) state. At pH 3.4, when the population of the U(A) becomes significant, the short-lifetime fluorescence comes predominantly from ANS binding to the U(A). Further lowering the pH leads to more exposure of the bound ANS. The long lifetime shifts toward and finally merges with the short lifetime and becomes one broad distribution that stands for ANS binding to the U(A) below pH 2.4. The above expanding-and-merging model is consistent with F-statistic analysis of NLLS models. The consistency of this model with the knowledge from the literature, as well as the continuity of the decay parameters changing upon experimental conditions are also crucial in drawing the conclusions.
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Affiliation(s)
- Gufeng Wang
- Department of Chemistry, the Center of Biocatalysis and Bioprocessing, and the Optical Science and Technology Center, University of Iowa, Iowa City, IA 52242, USA
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19
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Yamada Y, Yajima T, Fujiwara K, Arai M, Ito K, Shimizu A, Kihara H, Kuwajima K, Amemiya Y, Ikeguchi M. Helical and Expanded Conformation of Equine β-Lactoglobulin in the Cold-denatured State. J Mol Biol 2005; 350:338-48. [PMID: 15925384 DOI: 10.1016/j.jmb.2005.05.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2004] [Revised: 04/28/2005] [Accepted: 05/03/2005] [Indexed: 11/26/2022]
Abstract
The thermal unfolding transition of equine beta-lactoglobulin (ELG) was investigated by circular dichroism (CD) over a temperature range of -15 degrees C to 85 degrees C. In the presence of 2 M urea, a cooperative unfolding transition was observed both with increasing and decreasing temperature. The CD spectrum indicated that the heat and cold-denatured states of ELG have substantial secondary structures but lack persistent tertiary packing of the side-chains. In order to clarify the relation between the heat or cold-denatured state and the acid-denatured (A) state characterized previously, we have attempted to observe the temperature dependence of the CD spectrum at pH 1.5. The CD spectrum in the heat-denatured state is similar to that in the A state. The CD spectrum in the A state does not change cooperatively with increasing temperature. These results indicate that the heat-denatured state and the A state are the same structural state. On the other hand, the CD intensity at acid pH cooperatively increased with decreasing temperature. The CD spectrum at low temperature and acid pH is consistent with that in the cold-denatured state. Therefore, the cold-denatured state is distinguished from the heat-denatured state or the A state, and ELG assumes a larger amount of non-native alpha-helices in the cold-denatured state. Small angle X-ray scattering and analytical ultracentrifugation have indicated that ELG assumes an expanded chain-like conformation in the cold-denatured state in contrast to the compact globular conformation in the A state. The relation between the molecular size and the helical content in the partially folded states is discussed.
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Affiliation(s)
- Yoshiteru Yamada
- Department of Bioengineering, Graduate School of Engineering, Soka University, Hachioji, Tokyo 192-8577, Japan
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20
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Yang WY, Gruebele M. Kinetic equivalence of the heat and cold structural transitions of lambda6-85. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2005; 363:565-573. [PMID: 15664899 DOI: 10.1098/rsta.2004.1508] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Heat- and cold-denatured proteins are considered separate thermodynamic states because temperature tuning requires the protein to pass through two 'soft' first-order phase transitions. When both pressure and temperature changes are allowed, the heat- and cold-denatured states of proteins can be interconverted without going through the native state. This raises the question of whether these states are distinguished from one another by their folding kinetics. For the Tyr22Trp/Ala37Gly/Ala49Gly mutant of the 80 residue five-helix bundle protein lambda(6-85), we show that viscosity-corrected folding rates do not distinguish the cold- and heat-denatured states. We attribute this to a folding mechanism dominated by hydrophobic collapse. Our 'temperature-symmetric' approach offers an alternative to viscosity tuning with solvent additives in such cases.
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Affiliation(s)
- Wei Y Yang
- Center for Biophysics and Computational Biology, and Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
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21
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Taulier N, Beletskaya IV, Chalikian TV. Compressibility changes accompanying conformational transitions of apomyoglobin. Biopolymers 2005; 79:218-29. [PMID: 16100718 DOI: 10.1002/bip.20350] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We used high-precision density and ultrasonic velocity measurements to characterize the native (N), molten globule (MG), and unfolded (U) conformations of apomyoglobin. The molten globule states that were studied in this work include the MG(pH4)(NaCl) state observed at pH 4 and 20 mM NaCl, the MG(pH4)(NaTCA) state observed at pH 4 and 20 mM sodium trichloracetate (NaTCA), the MG(pH2)(NaCl) state observed at pH 2 and 200 mM NaCl, and the MG(pH2)(NaTCA) state observed at pH 2 and 20 mM NaTCA. We used our densimetric and acoustic data to evaluate changes in adiabatic compressibility associated with the acid- or salt-induced N-to-MG, MG-to-U, MG-to-MG, and U-to-MG transitions of the protein. The N-to-MG(pH4)(NaCl) and N-to-MG(pH4)(NaTCA) transitions are accompanied by decreases in compressibility of -(3.0 +/- 0.6) x 10(-6) and -(2.0 +/- 0.6) x 10(-6) cm3 g(-1)bar(-1), respectively. The N-to-MG(pH2)(NaCl) and N-to-MG(pH2)(NaTCA) transitions are associated with compressibility changes of -(4.9 +/- 1.1) x 10(-6) and (0.7 +/- 0.9) x 10(-6) cm3 g(-1) bar(-1), respectively. We interpret these data in terms of the degree of unfolding of the various molten globule forms of apomyoglobin. In general, our compressibility data reveal significant disparities between the various equilibrium molten globule states of apomyoglobin while also quantitatively characterizing each of these states. Volumetric insights provided by our data facilitate gaining a better understanding of the folding pathways, intermediates, and kinetics of apomyoglobin folding.
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Affiliation(s)
- Nicolas Taulier
- Department of Pharmaceutical Sciences, Leslie Dan Facultyof Pharmacy, University of Toronto, 19 Russell Street, Toronto, Ontario M5S 2S2, Canada
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22
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Choi HS, Huh J, Jo WH. Similarity of force-induced unfolding of apomyoglobin to its chemical-induced unfolding: an atomistic molecular dynamics simulation approach. Biophys J 2003; 85:1492-502. [PMID: 12944267 PMCID: PMC1303326 DOI: 10.1016/s0006-3495(03)74582-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
We have compared force-induced unfolding with traditional unfolding methods using apomyoglobin as a model protein. Using molecular dynamics simulation, we have investigated the structural stability as a function of the degree of mechanical perturbation. Both anisotropic perturbation by stretching two terminal atoms and isotropic perturbation by increasing the radius of gyration of the protein show the same key event of force-induced unfolding. Our primary results show that the native structure of apomyoglobin becomes destabilized against the mechanical perturbation as soon as the interhelical packing between the G and H helices is broken, suggesting that our simulation results share a common feature with the experimental observation that the interhelical contact is more important for the folding of apomyoglobin than the stability of individual helices. This finding is further confirmed by simulating both helix destabilizing and interhelical packing destabilizing mutants.
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Affiliation(s)
- Ho Sup Choi
- Hyperstructured Organic Materials Research Center, School of Material Science and Engineering, Seoul National University, Seoul 151-742, Korea
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23
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Ervin J, Larios E, Osváth S, Schulten K, Gruebele M. What causes hyperfluorescence: folding intermediates or conformationally flexible native states? Biophys J 2002; 83:473-83. [PMID: 12080134 PMCID: PMC1302161 DOI: 10.1016/s0006-3495(02)75183-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hyperfluorescent intensity maxima during protein unfolding titrations are often taken as a sign for a thermodynamic folding intermediate. Here we explore another possibility: that hyperfluorescence could be the signature of a "pretransition" conformationally loosened native state. To model such native states, we study mutants of a fluorescent ubiquitin variant, placing cavities at various distances from the tryptophan fluorophore. We examine the correlation between protein flexibility and enhanced fluorescence intensity by using circular dichroism, fluorescence intensity unfolding titrations, fluorescence anisotropy measurements, and molecular dynamics. Based on experiment and simulation, we propose a simple model for hyperfluorescence in terms of static and dynamic conformational properties of the native state during unfolding. Apomyoglobin denaturant unfolding and phosphoglycerate kinase cold denaturation are discussed as examples. Our results do not preclude the existence of thermodynamic intermediates but do raise caution that by itself, hyperfluorescence during unfolding titrations is not conclusive proof of thermodynamic folding intermediates.
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Affiliation(s)
- John Ervin
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Illinois 61801, USA
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24
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Haruta N, Kitagawa T. Time-resolved UV resonance Raman investigation of protein folding using a rapid mixer: characterization of kinetic folding intermediates of apomyoglobin. Biochemistry 2002; 41:6595-604. [PMID: 12022863 DOI: 10.1021/bi012027g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 244-nm excited transient UV resonance Raman spectra are observed for the refolding intermediates of horse apomyoglobin (h-apoMb) with a newly constructed mixed flow cell system, and the results are interpreted on the basis of the spectra observed for the equilibrium acid unfolding of the same protein. The dead time of mixing, which was determined with the appearance of UV Raman bands of imidazolium upon mixing of imidazole with acid, was 150 micros under the flow rate that was adopted. The pH-jump experiments of h-apoMb from pH 2.2 to 5.6 conducted with this device demonstrated the presence of three folding intermediates. On the basis of the analysis of W3 and W7 bands of Trp7 and Trp14, the first intermediate, formed before 250 micros, involved incorporation of Trp14 into the alpha-helix from a random coil. The frequency shift of the W3 band of Trp14 observed for this process was reproduced with a model peptide of the A helix when it forms the alpha-helix. In the second intermediate, formed around 1 ms after the start of refolding, the surroundings of both Trp7 and Trp14 were significantly hydrophobic, suggesting the formation of the hydrophobic core. In the third intermediate appearing around 3 ms, the hydrophobicity was relaxed to the same level as that of the pH 4 equilibrium intermediate, which was investigated in detail with the stationary state technique. The change from the third intermediate to the native state needs more time than 40 ms, while the appearance of the native spectrum after the mixing of the same solutions was confirmed separately.
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Affiliation(s)
- Nami Haruta
- School of Mathematical and Physical Sciences, The Graduate University for Advanced Studies, Myodaiji, Okazaki 444-8585, Japan
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25
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26
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Gilmanshin R, Gulotta M, Dyer RB, Callender RH. Structures of apomyoglobin's various acid-destabilized forms. Biochemistry 2001; 40:5127-36. [PMID: 11318634 DOI: 10.1021/bi002255v] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structures and the cold and hot melting thermodynamics of the acid- and salt-destabilized states of horse heart apomyoglobin (apoMb), including the E (extended) and various I forms, are studied using probes of tertiary structure (tryptophan fluorescence and FTIR spectroscopy) and secondary structure (far-UV CD and FTIR spectroscopy). These forms likely resemble early structures in the folding of the largely helical protein. Both the I and E forms retain the AGH core whereby the two ends of the protein are tied together with sufficient numbers of tertiary contacts, involving a number of hydrophobic residues, to show cooperative melting. The melting thermodynamics of E and I are distinctly different. E contains no other tertiary structure and probably little other secondary structure apart from the core. The more destabilized E form appears to contain "random" buried runs of polypeptide backbone which convert to alpha-helix in the I form(s). Most interestingly, E consists not of a single structure but is composed of a heterogeneous mixture of conformations, all showing corelike cooperative melting characteristics, and consisting presumably of varying contacts between the A portion of apomyoglobin and the G-H hairpin. These results bear on the energy landscape and structural features of the early part of apomyoglobin's folding pathway.
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Affiliation(s)
- R Gilmanshin
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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27
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Gulotta M, Gilmanshin R, Buscher TC, Callender RH, Dyer RB. Core formation in apomyoglobin: probing the upper reaches of the folding energy landscape. Biochemistry 2001; 40:5137-43. [PMID: 11318635 DOI: 10.1021/bi002256n] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An acid-destabilized form of apomyoglobin, the so-called E state, consists of a set of heterogeneous structures that are all characterized by a stable hydrophobic core composed of 30-40 residues at the intersection of the A, G, and H helices of the protein, with little other secondary structure and no other tertiary structure. Relaxation kinetics studies were carried out to characterize the dynamics of core melting and formation in this protein. The unfolding and/or refolding response is induced by a laser-induced temperature jump between the folded and unfolded forms of E, and structural changes are monitored using the infrared amide I' absorbance at 1648-1651 cm(-1) that reports on the formation of solvent-protected, native-like helix in the core and by fluorescence emission changes from apomyoglobin's Trp14, a measure of burial of the indole group of this residue. The fluorescence kinetics data are monoexponential with a relaxation time of 14 micros. However, infrared kinetics data are best fit to a biexponential function with relaxation times of 14 and 59 micros. These relaxation times are very fast, close to the limits placed on folding reactions by diffusion. The 14 micros relaxation time is weakly temperature dependent and thus represents a pathway that is energetically downhill. The appearance of this relaxation time in both the fluorescence and infrared measurements indicates that this folding event proceeds by a concomitant formation of compact secondary and tertiary structures. The 59 micros relaxation time is much more strongly temperature dependent and has no fluorescence counterpart, indicating an activated process with a large energy barrier wherein nonspecific hydrophobic interactions between helix A and the G and H helices cause some helix burial but Trp14 remains solvent exposed. These results are best fit by a multiple-pathway kinetic model when U collapses to form the various folded core structures of E. Thus, the results suggest very robust dynamics for core formation involving multiple folding pathways and provide significant insight into the primary processes of protein folding.
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Affiliation(s)
- M Gulotta
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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28
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Ervin J, Sabelko J, Gruebele M. Submicrosecond real-time fluorescence sampling: application to protein folding. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2000; 54:1-15. [PMID: 10739138 DOI: 10.1016/s1011-1344(00)00002-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Time-resolved fluorescence detection has become a central tool in the study of protein folding. This article briefly reviews modern fluorescence techniques and then focuses on recent improvements made possible by array photomultipliers, computer-controlled data gating, and long-memory multi-channel digitizers. It is now possible to detect fluorescence wavelength profiles and/or fluorescence decay transients very cost effectively with sub-microsecond kinetic time resolution out to long times. Folding kinetics can be analyzed by singular value decomposition (SVD) or chi-analysis. The latter provides an objective method for detecting nonexponential kinetics in two-state systems.
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Affiliation(s)
- J Ervin
- School of Chemical Sciences and Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana 61801, USA
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29
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Abstract
During protein folding, many of the events leading to secondary and tertiary structure occur in milliseconds or faster. Modern nuclear magnetic resonance and laser detection techniques, coupled with fast initiation of the folding reaction, are probing these events in great detail. Theory, ranging from analytical models to molecular dynamics calculations, is beginning to match up with experiment. As a result, timescales, from such elementary steps as the addition of a residue to a helix to strange kinetics of collapsing protein backbones, can now be measured and interpreted.
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Affiliation(s)
- M Gruebele
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, IL 61801, USA.
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30
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Chi Z, Asher SA. Ultraviolet resonance Raman examination of horse apomyoglobin acid unfolding intermediates. Biochemistry 1999; 38:8196-203. [PMID: 10387065 DOI: 10.1021/bi982654e] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have used UV resonance Raman spectroscopy to study the acid-induced denaturation of horse apomyoglobin (apoMb) between pH 7. 0 and 1.8. The 206.5 nm excited Raman spectra are dominated by amide vibrations, which are used to quantitatively determine the apoMb secondary structure. The 229 nm excited Raman spectra are dominated by the Tyr and Trp Raman bands, which are analyzed to examine changes of Tyr and Trp environments and solvent exposures. We observe two partially unfolded apoMb intermediates at pH 4 and pH 2, while we observe only one partially unfolded holoMb intermediate at 2, in which the G and H helices are mainly intact, while the rest of protein is unfolded. This partially unfolded holoMb intermediate at pH 2 is essentially identical to the pH 2 apoMb intermediate. The partially unfolded pH 4 apoMb intermediate is composed of the three folded A, G, and H helices and contains 38% helical structure. The changes in the Trp Raman cross sections during the acid-induced denaturation indicates that Trp 7 is likely to be fully exposed in the apoMb pH 4 intermediate and that the A helix melts with a pKa approximately 3.5.
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Affiliation(s)
- Z Chi
- Department of Chemistry, Chevron Science Center, University of Pittsburgh, Pennsylvania 15260, USA
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31
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Abstract
Highly nonexponential folding kinetics in aqueous solution have been observed during temperature jump-induced refolding of two proteins, yeast phosphoglycerate kinase and a ubiquitin mutant. The observations are most easily interpreted in terms of downhill folding, which posits a heterogeneous ensemble of structures en route to the folded state. The data are also reconciled with exponential kinetics measured under different experimental conditions and with titration experiments indicating cooperative folding.
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Affiliation(s)
- J Sabelko
- School of Chemical Sciences and Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, IL 61801, USA
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32
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Hardin C, Luthey-Schulten Z, Wolynes PG. Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides. Proteins 1999. [DOI: 10.1002/(sici)1097-0134(19990215)34:3<281::aid-prot2>3.0.co;2-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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33
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Gruebele M, Sabelko J, Ballew R, Ervin J. Laser Temperature Jump Induced Protein Refolding. Acc Chem Res 1998. [DOI: 10.1021/ar970083x] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Martin Gruebele
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61801
| | - Jobiah Sabelko
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61801
| | - Richard Ballew
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61801
| | - John Ervin
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61801
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