1
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Naidu KT, Prabhu NP. Polyols, increasing global stability of cytochrome c, destabilize the thermal unfolding intermediate. J Biomol Struct Dyn 2022; 40:11216-11228. [PMID: 34308796 DOI: 10.1080/07391102.2021.1956593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Studies on the intermediate states of proteins provide essential information on folding pathway and energy landscape of proteins. Osmolytes, known to alter the stability of proteins, might also affect the structure and energy states of folding intermediates. This was examined using cytochrome c (Cyt) as a model protein which forms a spectroscopically detectable intermediate during thermal denaturation transition. Most of the secondary structure and the native heme-ligation were intact in the intermediate state of the protein. Denaturants, urea and guanidinium hydrochloride, and ionic salt destabilizes the intermediate and drive the protein to follow two-state transition. The effect of polyol class of osmolytes, glycol, glycerol, erythritol, xylitol and sorbitol (with OH-groups two to six), on the intermediate was studied using Soret absorbance and far-UV circular dichroism. With the increasing concentration of any of the polyols, the transition-midpoint temperature (Tm) and the enthalpy change (ΔH) for native to intermediate transition were decreased. This indicated that the intermediate was destabilized by the polyols. However, the polyols increased the overall stability of the protein by increasing Tm and ΔH for intermediate to unfolded transition, except for glycol which destabilized the protein. These results show that the polyols could alter the energy state of the intermediate, and the effect of lower and higher polyols might be different on the stability and folding pathway of the protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- K Tejaswi Naidu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - N Prakash Prabhu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
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2
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Zhou M, Jiao L, Xu S, Xu Y, Du M, Zhang X, Kong X. A novel method for photon unfolding spectroscopy of protein ions in the gas phase. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:043003. [PMID: 35489914 DOI: 10.1063/5.0080040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
In this study, a new experimental method for photon unfolding spectroscopy of protein ions based on a Fourier transform ion cyclotron resonance (FT ICR) mass spectrometer was developed. The method of short-time Fourier transform has been applied here to obtain decay curves of target ions trapped in the cell of the FT ICR mass spectrometer. Based on the decay constants, the collision cross sections (CCSs) of target ions were calculated using the energetic hard-sphere model. By combining a tunable laser to the FT ICR mass spectrometer, the changes of CCSs of the target ions were recorded as a function of the wavelengths; thus, the photon isomerization spectrum was obtained. As one example, the photon isomerization spectrum of [Cyt c + 13H]13+ was recorded as the decay constants relative to the applied wavelengths of the laser in the 410-480 nm range. The spectrum shows a maximum at 426 nm, where an unfolded structure induced by a 4 s irradiation can be deduced. The strong peak at 426 nm was also observed for another ion of [Cyt c + 15H]15+, although some difference at 410 nm between the two spectra was found at the same time. This novel method can be expanded to ultraviolet or infrared region, making the experimental study of wavelength-dependent photon-induced structural variation of a variety of organic or biological molecules possible.
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Affiliation(s)
- Min Zhou
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
| | - Luyang Jiao
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
| | - Shiyin Xu
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
| | - Yicheng Xu
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
| | - Mengying Du
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
| | - Xianyi Zhang
- School of Physics and Electronic Information, Anhui Normal University, Wuhu 241000, China
| | - Xianglei Kong
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
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3
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Mizukami T, Bedford JT, Liao S, Greene LH, Roder H. Effects of ionic strength on the folding and stability of SAMP1, a ubiquitin-like halophilic protein. Biophys J 2022; 121:552-564. [PMID: 35063455 PMCID: PMC8874027 DOI: 10.1016/j.bpj.2022.01.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/13/2021] [Accepted: 01/13/2022] [Indexed: 11/21/2022] Open
Abstract
Our knowledge of the folding behavior of proteins from extremophiles is limited at this time. These proteins may more closely resemble the primordial proteins selected in early evolution under extreme conditions. The small archaeal modifier protein 1 (SAMP1) studied in this report is an 87-residue protein with a β-grasp fold found in the halophile Haloferax volcanii from the Dead Sea. To gain insight into the effects of salt on the stability and folding mechanism of SAMP1, we conducted equilibrium and kinetic folding experiments as a function of sodium chloride concentration. The results revealed that increasing ionic strength accelerates refolding and slows down unfolding of SAMP1, giving rise to a pronounced salt-induced stabilization. With increasing NaCl concentration, the rate of folding observed via a combination of continuous-flow (0.1-2 ms time range) and stopped-flow measurements (>2 ms) exhibited a >100-fold increase between 0.1 and 1.5 M NaCl and leveled off at higher concentrations. Using the Linderström-Lang smeared charge formalism to model electrostatic interactions in ground and transition states encountered during folding, we showed that the observed salt dependence is dominated by Debye-Hückel screening of electrostatic repulsion among numerous negatively charged residues. Comparisons are also drawn with three well-studied mesophilic members of the β-grasp superfamily: protein G, protein L, and ubiquitin. Interestingly, the folding rate of SAMP1 in 3 M sodium chloride is comparable to that of protein G, ubiquitin, and protein L at lower ionic strength. The results indicate the important role of electrostatic interactions in protein folding and imply that proteins have evolved to minimize unfavorable charge-charge interactions under their specific native conditions.
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Affiliation(s)
- Takuya Mizukami
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - John T Bedford
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia
| | - ShanHui Liao
- School of Life Sciences, University of Science and Technology of China, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Science, Hefei, Anhui, P.R. China
| | - Lesley H Greene
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia.
| | - Heinrich Roder
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania.
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4
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Hossain SS, Paul S, Samanta A. Structural Stability and Conformational Dynamics of Cytochrome c in Hydrated Deep Eutectic Solvents. J Phys Chem B 2021; 125:5757-5765. [PMID: 34042450 DOI: 10.1021/acs.jpcb.1c01975] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many deep eutectic solvents (DESs) are currently being explored as environment-friendly media for biorelated applications. As an understanding of the effect of these solvents on the structure of biomolecules is crucial for these applications, we study how two DESs comprising trimethylglycine (TMG) and ethylene glycol (EG) or glycerol (GL) influence the structural stability and conformational dynamics of cytochrome c (Cytc) using single-molecule-based fluorescence correlation spectroscopy (FCS) technique and several other ensemble-based biophysical methods. The FCS studies on A488-labeled Cytc enable an estimation of the size (20.5 ± 1.5 Å) of the protein and capture its conformational dynamics (54 ± 2 μs) in aqueous buffered solution. It is observed that both size and conformational dynamics of the protein are influenced in the presence of the DESs, but this effect is more pronounced in the case of TMG-EG. The ensemble measurements on both labeled and wild-type Cytc reveal that the protein structure is unfolded completely by TMG-EG, whereas the structure is slightly altered by TMG-GL. The results suggest that the behavior of Cytc in hydrated DESs is determined by the strength of interactions between the DES constituents as well as that between the constituents and the water molecules present in the system.
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Affiliation(s)
- Sk Saddam Hossain
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Sneha Paul
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Anunay Samanta
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
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5
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Pabbathi A, Samanta A. On the Stability and Conformational Dynamics of Cytochrome c in Ammonium Ionic Liquids. J Phys Chem B 2020; 124:8132-8140. [PMID: 32830967 DOI: 10.1021/acs.jpcb.0c05633] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Owing to their potential applications in the extraction, purification, and preservation of biomolecules and biocatalysis, ionic liquids (ILs) have gained great attention in biotechnology. Although it is known that the structure and dynamics of proteins in ILs depend on the nature of both proteins and ILs, the biophysical mechanism governing the protein-IL interaction, which determines the stability of proteins or the activity of an enzyme in these nonconventional media, is yet to be understood clearly. Herein, we study the effect of two ammonium ILs, triethylammonium dihydrogen phosphate (TEAP) and tributylammonium dihydrogen phosphate (TBAP), on the stability and conformational dynamics of cytochrome c (Cyt c) in its native and unfolded states, employing primarily the single molecule-based fluorescence correlation spectroscopy (FCS) technique. The results show that the native structure of Cyt c is not significantly altered by TEAP, but the tertiary structure is perturbed to a great extent by TBAP, which comprises a longer alkyl chain. Fluctuations of the fluorescence intensity of Alexa488 dye-labeled Cyt c in FCS measurements reveal conformational dynamics (67 ± 10 μs) in the native state of Cyt c that is accelerated in the presence of both ILs but not affected when Cyt c is in its unfolded state. The present findings demonstrate how the stability of this protein can be modulated by using ammonium ILs of different alkyl chain lengths.
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Affiliation(s)
- Ashok Pabbathi
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Anunay Samanta
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
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6
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Takekiyo T, Miyazaki K, Watanabe Y, Uesugi Y, Tanaka S, Ishikawa Y, Yoshimura Y. Solubilization and recovery of heat-aggregated cytochrome c using alkylammonium nitrate. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111239] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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7
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Khan SH, Prakash A, Pandey P, Lynn AM, Islam A, Hassan MI, Ahmad F. Protein folding: Molecular dynamics simulations and in vitro studies for probing mechanism of urea- and guanidinium chloride-induced unfolding of horse cytochrome-c. Int J Biol Macromol 2019; 122:695-704. [DOI: 10.1016/j.ijbiomac.2018.10.186] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/27/2018] [Accepted: 10/27/2018] [Indexed: 11/26/2022]
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8
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Konno S, Doi K, Ishimori K. Uncovering dehydration in cytochrome c refolding from urea- and guanidine hydrochloride-denatured unfolded state by high pressure spectroscopy. Biophys Physicobiol 2019; 16:18-27. [PMID: 30775200 PMCID: PMC6373425 DOI: 10.2142/biophysico.16.0_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 12/16/2018] [Indexed: 12/01/2022] Open
Abstract
To investigate the dehydration associated with protein folding, the partial molar volume changes for protein unfolding (ΔVu) in cytochrome c (Cyt c) were determined using high pressure absorption spectroscopy. ΔVu values for the unfolding to urea- and guanidine hydrochloride (GdnHCl)-denatured Cyt c were estimated to be 56±5 and 29±1 mL mol−1, respectively. Considering that the volume change for hydration of hydrophobic groups is positive and that Cyt c has a covalently bonded heme, a positive ΔVu reflects the primary contribution of the hydration of heme. Because of the marked tendency of guanidium ions to interact with hydrophobic groups, a smaller number of water molecules were hydrated with hydrophobic groups in GdnHCl-denatured Cyt c than in urea-denatured Cyt c, resulting in the smaller positive ΔVu. On the other hand, urea is a relatively weak denaturant and urea-denatured Cyt c is not completely hydrated, which retains the partially folded structures. To unfold such partial structures, we introduced a mutation near the heme binding site, His26, to Gln, resulting in a negatively shifted ΔVu (4±2 mL mol−1) in urea-denatured Cyt c. The formation of the more solvated and less structured state in the urea-denatured mutant enhanced hydration to the hydrophilic groups in the unfolding process. Therefore, we confirmed the hydration of amino acid residues in the protein unfolding of Cyt c by estimating ΔVu, which allows us to discuss the hydrated structures in the denatured states of proteins.
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Affiliation(s)
- Shohei Konno
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Kentaro Doi
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Koichiro Ishimori
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan.,Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
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9
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Mizukami T, Xu M, Fazlieva R, Bychkova VE, Roder H. Complex Folding Landscape of Apomyoglobin at Acidic pH Revealed by Ultrafast Kinetic Analysis of Core Mutants. J Phys Chem B 2018; 122:11228-11239. [PMID: 30133301 DOI: 10.1021/acs.jpcb.8b06895] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Under mildly acidic conditions (pH 4-4.5) apomyoglobin (apoMb) adopts a partially structured equilibrium state ( M-state) that structurally resembles a kinetic intermediate encountered at a late stage of folding to the native structure at neutral pH. We have previously reported that the M-state is formed rapidly (<1 ms) via a multistate process and thus offers a unique opportunity for exploring early stages of folding by both experimental and computational techniques. In order to gain structural insight into intermediates and barriers at the residue level, we studied the folding/unfolding kinetics of 12 apoMb mutants at pH 4.2 using fluorescence-detected ultrafast mixing techniques. Global analysis of the submillisecond folding/unfolding kinetics vs urea concentration for each variant, based on a sequential four-state mechanism ( U ⇔ I ⇔ L ⇔ M), allowed us to determine elementary rate constants and their dependence on urea concentration for most transitions. Comparison of the free energy diagrams constructed from the kinetic data of the mutants with that of wild-type apoMb yielded quantitative information on the effects of mutations on the free energy (ΔΔ G) of both intermediates and the first two kinetic barriers encountered during folding. Truncation of conserved aliphatic side chains on helices A, G, and H gives rise to a stepwise increase in ΔΔ G as the protein advances from U toward M, consistent with progressive stabilization of native-like contacts within the primary core of apoMb. Helix-helix contacts in the primary core contribute little to the first folding barrier ( U ⇔ I) and thus are not required for folding initiation but are critical for the stability of the late intermediate, L, and the M-state. Alanine substitution of hydrophobic residues at more peripheral helix-helix contact sites of the native structure, which are still absent or unstable in the M-state, shows both positive (destabilizing) and negative (stabilizing) ΔΔ G, indicating that non-native contacts are formed initially and weakened or lost as a result of subsequent structural rearrangement steps.
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Affiliation(s)
- Takuya Mizukami
- Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , Pennsylvania 19111 , United States
| | - Ming Xu
- Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , Pennsylvania 19111 , United States
| | - Ruzaliya Fazlieva
- Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , Pennsylvania 19111 , United States
| | - Valentina E Bychkova
- Laboratory of Protein Physics , Institute of Protein Science, Russian Academy of Sciences , Pushchino , Moscow Region 142290 , Russia
| | - Heinrich Roder
- Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , Pennsylvania 19111 , United States
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10
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Danielson TA, Stine JM, Dar TA, Briknarova K, Bowler BE. Effect of an Imposed Contact on Secondary Structure in the Denatured State of Yeast Iso-1-cytochrome c. Biochemistry 2017; 56:6662-6676. [PMID: 29148740 DOI: 10.1021/acs.biochem.7b01002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There is considerable evidence that long-range interactions stabilize residual protein structure under denaturing conditions. However, evaluation of the effect of a specific contact on structure in the denatured state has been difficult. Iso-1-cytochrome c variants with a Lys54 → His mutation form a particularly stable His-heme loop in the denatured state, suggestive of loop-induced residual structure. We have used multidimensional nuclear magnetic resonance methods to assign 1H and 15N backbone amide and 13C backbone and side chain chemical shifts in the denatured state of iso-1-cytochrome c carrying the Lys54 → His mutation in 3 and 6 M guanidine hydrochloride and at both pH 6.4, where the His54-heme loop is formed, and pH 3.6, where the His54-heme loop is broken. Using the secondary structure propensity score, with the 6 M guanidine hydrochloride chemical shift data as a random coil reference state for data collected in 3 M guanidine hydrochloride, we found residual helical structure in the denatured state for the 60s helix and the C-terminal helix, but not in the N-terminal helix in the presence or absence of the His54-heme loop. Non-native helical structure is observed in two regions that form Ω-loops in the native state. There is more residual helical structure in the C-terminal helix at pH 6.4 when the loop is formed. Loop formation also appears to stabilize helical structure near His54, consistent with induction of helical structure observed when His-heme bonds form in heme-peptide model systems. The results are discussed in the context of the folding mechanism of cytochrome c.
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Affiliation(s)
- Travis A Danielson
- Department of Chemistry and Biochemistry, University of Montana , Missoula, Montana 59812, United States
| | - Jessica M Stine
- Department of Chemistry and Biochemistry, University of Montana , Missoula, Montana 59812, United States
| | - Tanveer A Dar
- Department of Chemistry and Biochemistry, University of Montana , Missoula, Montana 59812, United States
| | - Klara Briknarova
- Department of Chemistry and Biochemistry, University of Montana , Missoula, Montana 59812, United States.,Center for Biomolecular Structure and Dynamics, University of Montana , Missoula, Montana 59812, United States
| | - Bruce E Bowler
- Department of Chemistry and Biochemistry, University of Montana , Missoula, Montana 59812, United States.,Center for Biomolecular Structure and Dynamics, University of Montana , Missoula, Montana 59812, United States
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11
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Singh SM, Bandi S, Jones DNM, Mallela KMG. Effect of Polysorbate 20 and Polysorbate 80 on the Higher-Order Structure of a Monoclonal Antibody and Its Fab and Fc Fragments Probed Using 2D Nuclear Magnetic Resonance Spectroscopy. J Pharm Sci 2017; 106:3486-3498. [PMID: 28843351 DOI: 10.1016/j.xphs.2017.08.011] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 08/15/2017] [Accepted: 08/17/2017] [Indexed: 10/19/2022]
Abstract
We examined how polysorbate 20 (PS20; Tween 20) and polysorbate 80 (PS80; Tween 80) affect the higher-order structure of a monoclonal antibody (mAb) and its antigen-binding (Fab) and crystallizable (Fc) fragments, using near-UV circular dichroism and 2D nuclear magnetic resonance (NMR). Both polysorbates bind to the mAb with submillimolar affinity. Binding causes significant changes in the tertiary structure of mAb with no changes in its secondary structure. 2D 13C-1H methyl NMR indicates that with increasing concentration of polysorbates, the Fab region showed a decrease in crosspeak volumes. In addition to volume changes, PS20 caused significant changes in the chemical shifts compared to no changes in the case of PS80. No such changes in crosspeak volumes or chemical shifts were observed in the case of Fc region, indicating that polysorbates predominantly affect the Fab region compared to the Fc region. This differential effect of polysorbates on the Fab and Fc regions was because of the lesser thermodynamic stability of the Fab compared to the Fc. These results further indicate that PS80 is the preferred polysorbate for this mAb formulation, because it offers higher protection against aggregation, causes lesser structural perturbation, and has weaker binding affinity with fewer binding sites compared to PS20.
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Affiliation(s)
- Surinder M Singh
- Department of Pharmaceutical Sciences and Center for Pharmaceutical Biotechnology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Swati Bandi
- Department of Pharmaceutical Sciences and Center for Pharmaceutical Biotechnology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - David N M Jones
- Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045; Program in Structural Biology and Biochemistry, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Krishna M G Mallela
- Department of Pharmaceutical Sciences and Center for Pharmaceutical Biotechnology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045; Program in Structural Biology and Biochemistry, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045.
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12
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Takekiyo T, Ishikawa Y, Yoshimura Y. Cryopreservation of Proteins Using Ionic Liquids: A Case Study of Cytochrome c. J Phys Chem B 2017; 121:7614-7620. [DOI: 10.1021/acs.jpcb.7b05158] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Takahiro Takekiyo
- Department of Applied Chemistry, National Defense Academy, 1-10-20, Hashirimizu, Yokosuka,
Kanagawa 239-8686, Japan
| | - Yuka Ishikawa
- Department of Applied Chemistry, National Defense Academy, 1-10-20, Hashirimizu, Yokosuka,
Kanagawa 239-8686, Japan
| | - Yukihiro Yoshimura
- Department of Applied Chemistry, National Defense Academy, 1-10-20, Hashirimizu, Yokosuka,
Kanagawa 239-8686, Japan
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13
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Wahiduzzaman, Dar MA, Haque MA, Idrees D, Hassan MI, Islam A, Ahmad F. Characterization of folding intermediates during urea-induced denaturation of human carbonic anhydrase II. Int J Biol Macromol 2017; 95:881-887. [DOI: 10.1016/j.ijbiomac.2016.10.073] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 10/07/2016] [Accepted: 10/22/2016] [Indexed: 11/25/2022]
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14
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Adhikary R, Zimmermann J, Romesberg FE. Transparent Window Vibrational Probes for the Characterization of Proteins With High Structural and Temporal Resolution. Chem Rev 2017; 117:1927-1969. [DOI: 10.1021/acs.chemrev.6b00625] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jörg Zimmermann
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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15
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Halim AAA, Zaroog MS, Kadir HA, Tayyab S. Alcohol-induced structural transitions in the acid-denatured Bacillus licheniformis α-amylase. JOURNAL OF SAUDI CHEMICAL SOCIETY 2017. [DOI: 10.1016/j.jscs.2014.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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16
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Word TA, Larsen RW. Time resolved calorimetry of photo-induced folding in horse heart cytochrome c at high pH. Arch Biochem Biophys 2016; 615:10-14. [PMID: 28041937 DOI: 10.1016/j.abb.2016.12.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/27/2016] [Accepted: 12/28/2016] [Indexed: 10/20/2022]
Abstract
Here the molar volume and enthalpy changes associated with the early events in the folding of ferrocytochrome c (Cc) at high pH have been examined using time resolved photoacoustic calorimetry (PAC). The data reveal an overall volume change of 1.3 ± 0.3 mL mol-1 and an enthalpy change of 13 ± 7 kcal mol -1 occurring subsequent to photodissociation of the unfolded CO bound Cc species in <∼20 ns. Two additional kinetic phases are observed that are associated with non-native His binding (ΔH and ΔV of 2 ± 4 kcal mol-1 and -0.5 mL mol-1, τ ∼ 2.5 μs ) and Met binding (ΔH and ΔV -0.4 ± 2 kcal mol-1 and -0.1 ± 0.1 mL mol-1, τ∼ 660 ns). Considering only protein conformational changes (excluding volume and enthalpies associated with heme ligation events) the initial conformational event exhibits a ΔH and ΔV of 6 ± 3 kcal mol-1 and -3±0.1 mL mol-1, respectively, that are attributed to a small contraction of the unfolded protein. The corresponding enthalpy associated with both native and non-native ligand binding are found to be -5±4 kcal mol-1 (Fe-Met) and +20 ± 4 kcal mol-1 (Fe-His) with the change in volume for both phases being essential negligible. This would indicate that non-native ligand binding likely occurs from an already collapsed conformation.
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Affiliation(s)
- Tarah A Word
- Department of Chemistry, University of South Florida, 4202 East Fowler Ave., Tampa, FL 33602 USA
| | - Randy W Larsen
- Department of Chemistry, University of South Florida, 4202 East Fowler Ave., Tampa, FL 33602 USA.
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17
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Kabir A, Honda RP, Kamatari YO, Endo S, Fukuoka M, Kuwata K. Effects of ligand binding on the stability of aldo-keto reductases: Implications for stabilizer or destabilizer chaperones. Protein Sci 2016; 25:2132-2141. [PMID: 27595938 PMCID: PMC5119574 DOI: 10.1002/pro.3036] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/30/2016] [Indexed: 01/26/2023]
Abstract
Ligands such as enzyme inhibitors stabilize the native conformation of a protein upon binding to the native state, but some compounds destabilize the native conformation upon binding to the non-native state. The former ligands are termed "stabilizer chaperones" and the latter ones "destabilizer chaperones." Because the stabilization effects are essential for the medical chaperone (MC) hypothesis, here we have formulated a thermodynamic system consisting of a ligand and a protein in its native- and non-native state. Using the differential scanning fluorimetry and the circular dichroism varying the urea concentration and temperature, we found that when the coenzyme NADP+ was absent, inhibitors such as isolithocholic acid stabilized the aldo-keto reductase AKR1A1 upon binding, which showed actually the three-state folding, but destabilized AKR1B10. In contrast, in the presence of NADP+ , they destabilized AKR1A1 and stabilized AKR1B10. To explain these phenomena, we decomposed the free energy of stabilization (ΔΔG) into its enthalpy (ΔΔH) and entropy (ΔΔS) components. Then we found that in a relatively unstable protein showing the three-state folding, native conformation was stabilized by the negative ΔΔH in association with the negative ΔΔS, suggesting that the stabilizer chaperon decreases the conformational fluctuation of the target protein or increase its hydration. However, in other cases, ΔΔG was essentially determined by the delicate balance between ΔΔH and ΔΔS. The proposed thermodynamic formalism is applicable to the system including multiple ligands with allosteric interactions. These findings would promote the development of screening strategies for MCs to regulate the target conformations.
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Affiliation(s)
- Aurangazeb Kabir
- United Graduate School of Drug Discovery and Medical Information SciencesGifu UniversityGifu501‐1193Japan
| | - Ryo P. Honda
- Department of Molecular Pathobiochemistry, Graduate School of MedicineGifu UniversityGifu501‐1193Japan
| | | | - Satoshi Endo
- Laboratory of BiochemistryGifu Pharmaceutical UniversityGifu501‐1196Japan
| | - Mayuko Fukuoka
- United Graduate School of Drug Discovery and Medical Information SciencesGifu UniversityGifu501‐1193Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information SciencesGifu UniversityGifu501‐1193Japan
- Department of Gene and Development, Graduate School of MedicineGifu UniversityGifu501‐1193Japan
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18
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Characterisation of molten globule-like state of sheep serum albumin at physiological pH. Int J Biol Macromol 2016; 89:605-13. [PMID: 27180298 DOI: 10.1016/j.ijbiomac.2016.05.036] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/05/2016] [Accepted: 05/10/2016] [Indexed: 01/26/2023]
Abstract
Sheep serum albumin (SSA) is a 583 amino acid residues long multidomain monomeric protein which is rich in cysteine and low in tryptophan content. The serum albumins (from human, bovine and sheep) play a vital role among all proteins investigated until now, as they are the most copious circulatory proteins. We have purified SSA from sheep kidneys by a simple and efficient two-step purification procedure. Further, we have studied urea-induced denaturation of SSA by monitoring changes in the difference absorption coefficient at 287nm (Δε287), intrinsic fluorescence emission intensity at 347nm (F347) and mean residue ellipticity at 222nm ([θ]222) at pH 7.4 and 25°C. The coincidence of denaturation curves of these optical properties suggests that urea-induced denaturation is a bi-phasic process (native (N) state↔intermediate (X) state↔denatured (D) state) with a stable intermediate populated around 4.2-4.7M urea. The intermediate (X) state was further characterized by the far-UV and near-UV CD, dynamic light scattering (DLS) and fluorescence using 1-anilinonaphthalene-8-sulfonic acid (ANS) binding method. All denaturation curves were analyzed for Gibbs free energy changes associated with the equilibria, N state↔X state and X state↔D state in the absence of urea.
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19
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Jain R, Kumar R, Kumar S, Chhabra R, Agarwal MC, Kumar R. Analysis of the pH-dependent stability and millisecond folding kinetics of horse cytochrome c. Arch Biochem Biophys 2015; 585:52-63. [DOI: 10.1016/j.abb.2015.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Revised: 09/10/2015] [Accepted: 09/14/2015] [Indexed: 11/26/2022]
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20
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Molinas MF, Benavides L, Castro MA, Murgida DH. Stability, redox parameters and electrocatalytic activity of a cytochrome domain from a new subfamily. Bioelectrochemistry 2015; 105:25-33. [DOI: 10.1016/j.bioelechem.2015.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 04/21/2015] [Accepted: 05/03/2015] [Indexed: 11/24/2022]
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21
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Gam J, Ha JS, Kim H, Lee DH, Lee J, Lee SG. Ratiometric analyses at critical temperatures can magnify the signal intensity of FRET-based sugar sensors with periplasmic binding proteins. Biosens Bioelectron 2015; 72:37-43. [DOI: 10.1016/j.bios.2015.04.083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 04/24/2015] [Accepted: 04/25/2015] [Indexed: 11/29/2022]
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22
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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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23
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Kubo T, Arimura S, Tominaga Y, Naito T, Hosoya K, Otsuka K. Molecularly Imprinted Polymers for Selective Adsorption of Lysozyme and Cytochrome c Using a PEG-Based Hydrogel: Selective Recognition for Different Conformations Due to pH Conditions. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b00834] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Takuya Kubo
- Graduate
School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Shunsuke Arimura
- Graduate
School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yuichi Tominaga
- Structural
Materials Research Institute, National Institute of Advanced Industrial Science and Technology, 2266-98 Anagahora, Shimoshidami, Moriyama-ku, Nagoya 463-8560, Japan
| | - Toyohiro Naito
- Graduate
School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Ken Hosoya
- Graduate
School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Shimogamo
Hangicho, Kyoto 606-8522, Japan
| | - Koji Otsuka
- Graduate
School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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24
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Rahaman H, Alam Khan MK, Hassan MI, Islam A, Moosavi-Movahedi AA, Ahmad F. Heterogeneity of equilibrium molten globule state of cytochrome c induced by weak salt denaturants under physiological condition. PLoS One 2015; 10:e0120465. [PMID: 25849212 PMCID: PMC4388492 DOI: 10.1371/journal.pone.0120465] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 01/22/2015] [Indexed: 12/12/2022] Open
Abstract
While many proteins are recognized to undergo folding via intermediate(s), the heterogeneity of equilibrium folding intermediate(s) along the folding pathway is less understood. In our present study, FTIR spectroscopy, far- and near-UV circular dichroism (CD), ANS and tryptophan fluorescence, near IR absorbance spectroscopy and dynamic light scattering (DLS) were used to study the structural and thermodynamic characteristics of the native (N), denatured (D) and intermediate state (X) of goat cytochorme c (cyt-c) induced by weak salt denaturants (LiBr, LiCl and LiClO4) at pH 6.0 and 25°C. The LiBr-induced denaturation of cyt-c measured by Soret absorption (Δε400) and CD ([θ]409), is a three-step process, N ↔ X ↔ D. It is observed that the X state obtained along the denaturation pathway of cyt-c possesses common structural and thermodynamic characteristics of the molten globule (MG) state. The MG state of cyt-c induced by LiBr is compared for its structural and thermodynamic parameters with those found in other solvent conditions such as LiCl, LiClO4 and acidic pH. Our observations suggest: (1) that the LiBr-induced MG state of cyt-c retains the native Met80-Fe(III) axial bond and Trp59-propionate interactions; (2) that LiBr-induced MG state of cyt-c is more compact retaining the hydrophobic interactions in comparison to the MG states induced by LiCl, LiClO4 and 0.5 M NaCl at pH 2.0; and (3) that there exists heterogeneity of equilibrium intermediates along the unfolding pathway of cyt-c as highly ordered (X1), classical (X2) and disordered (X3), i.e., D ↔ X3 ↔ X2 ↔ X1 ↔ N.
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Affiliation(s)
- Hamidur Rahaman
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Md. Khurshid Alam Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Md. 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
- * E-mail:
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25
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Roy S, Basu S, Datta AK, Bhattacharyya D, Banerjee R, Dasgupta D. Equilibrium unfolding of cyclophilin from Leishmania donovani: characterization of intermediate states. Int J Biol Macromol 2014; 69:353-60. [PMID: 24887548 DOI: 10.1016/j.ijbiomac.2014.05.063] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 05/20/2014] [Accepted: 05/24/2014] [Indexed: 10/25/2022]
Abstract
Cyclophilin from Leishmania donovani (LdCyp) is a ubiquitous peptidyl-prolyl cis-trans isomerase involved in a host of important cellular activities, such as signaling, heat shock response, chaperone activity, mitochondrial pore maintenance and regulation of HIV-1 infectivity. It also acts as the prime cellular target for the auto-immune drug cyclosporine A (CsA). LdCyp is composed of a beta barrel encompassing the unique hydrophobic core of the molecule and is flanked by two helices (H1, H2) on either end of the barrel. The protein contains a lone partially exposed tryptophan. In the present work the equilibrium unfolding of LdCyp has been studied by fluorescence, circular dichroism and the non-coincidence of their respective Cm's, indicates a non-two state transition. This fact was further corroborated by binding studies of the protein with bis-ANS and the lack of an isochromatic point in far UV CD. The thermal stability of the possible intermediates was characterized by differential scanning calorimetry. Further, MD simulations performed at 310, 400 and 450K exhibited the tendency of both helices to partially unwind and adopt non-native geometries with respect to the core, quite early in the unfolding process, in contrast to the relatively stable beta barrel.
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Affiliation(s)
- Sourav Roy
- Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, West Bengal, India
| | - Sankar Basu
- Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, West Bengal, India
| | - Alok K Datta
- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | | | - Rahul Banerjee
- Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, West Bengal, India.
| | - Dipak Dasgupta
- Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, West Bengal, India.
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26
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Kathuria SV, Kayatekin C, Barrea R, Kondrashkina E, Graceffa R, Guo L, Nobrega RP, Chakravarthy S, Matthews CR, Irving TC, Bilsel O. Microsecond barrier-limited chain collapse observed by time-resolved FRET and SAXS. J Mol Biol 2014; 426:1980-94. [PMID: 24607691 DOI: 10.1016/j.jmb.2014.02.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 02/14/2014] [Accepted: 02/24/2014] [Indexed: 01/08/2023]
Abstract
It is generally held that random-coil polypeptide chains undergo a barrier-less continuous collapse when the solvent conditions are changed to favor the fully folded native conformation. We test this hypothesis by probing intramolecular distance distributions during folding in one of the paradigms of folding reactions, that of cytochrome c. The Trp59-to-heme distance was probed by time-resolved Förster resonance energy transfer in the microsecond time range of refolding. Contrary to expectation, a state with a Trp59-heme distance close to that of the guanidinium hydrochloride (GdnHCl) denatured state is present after ~27 μs of folding. A concomitant decrease in the population of this state and an increase in the population of a compact high-FRET (Förster resonance energy transfer) state (efficiency>90%) show that the collapse is barrier limited. Small-angle X-ray scattering (SAXS) measurements over a similar time range show that the radius of gyration under native favoring conditions is comparable to that of the GdnHCl denatured unfolded state. An independent comprehensive global thermodynamic analysis reveals that marginally stable partially folded structures are also present in the nominally unfolded GdnHCl denatured state. These observations suggest that specifically collapsed intermediate structures with low stability in rapid equilibrium with the unfolded state may contribute to the apparent chain contraction observed in previous fluorescence studies using steady-state detection. In the absence of significant dynamic averaging of marginally stable partially folded states and with the use of probes sensitive to distance distributions, barrier-limited chain contraction is observed upon transfer of the GdnHCl denatured state ensemble to native-like conditions.
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Affiliation(s)
- Sagar V Kathuria
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Can Kayatekin
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Raul Barrea
- BioCAT, CSRRI, Illinois Institute of Technology, Chicago, IL 60616, USA
| | | | - Rita Graceffa
- BioCAT, CSRRI, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Liang Guo
- BioCAT, CSRRI, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - R Paul Nobrega
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | | - C Robert Matthews
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Thomas C Irving
- BioCAT, CSRRI, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Osman Bilsel
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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27
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Kumar S, Sharma D, Kumar R. Effect of urea and alkylureas on the stability and structural fluctuation of the M80-containing Ω-loop of horse cytochrome c. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:641-55. [DOI: 10.1016/j.bbapap.2014.01.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 01/10/2014] [Accepted: 01/22/2014] [Indexed: 11/27/2022]
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28
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Liu H, Dong C, Ren J. Tempo-Spatially Resolved Scattering Correlation Spectroscopy under Dark-Field Illumination and Its Application to Investigate Dynamic Behaviors of Gold Nanoparticles in Live Cells. J Am Chem Soc 2014; 136:2775-85. [DOI: 10.1021/ja410284j] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Heng Liu
- College of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiaotong University, Shanghai 200240, People’s Republic of China
| | - Chaoqing Dong
- College of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiaotong University, Shanghai 200240, People’s Republic of China
| | - Jicun Ren
- College of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiaotong University, Shanghai 200240, People’s Republic of China
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29
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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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30
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Fazelinia H, Xu M, Cheng H, Roder H. Ultrafast hydrogen exchange reveals specific structural events during the initial stages of folding of cytochrome c. J Am Chem Soc 2013; 136:733-40. [PMID: 24364692 DOI: 10.1021/ja410437d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Many proteins undergo a sharp decrease in chain dimensions during early stages of folding, prior to the rate-limiting step in folding. However, it remains unclear whether compact states are the result of specific folding events or a general hydrophobic collapse of the poly peptide chain driven by the change in solvent conditions. To address this fundamental question, we extended the temporal resolution of NMR-detected H/D exchange labeling experiments into the microsecond regime by adopting a microfluidics approach. By observing the competition between H/D exchange and folding as a function of labeling pH, coupled with direct measurement of exchange rates in the unfolded state, we were able to monitor hydrogen-bond formation for over 50 individual backbone NH groups within the initial 140 microseconds of folding of horse cytochrome c. Clusters of solvent-shielded amide protons were observed in two α-helical segments in the C-terminal half of the protein, while the N-terminal helix remained largely unstructured, suggesting that proximity in the primary structure is a major factor in promoting helix formation and association at early stages of folding, while the entropically more costly long-range contacts between the N- and C-terminal helices are established only during later stages. Our findings clearly indicate that the initial chain condensation in cytochrome c is driven by specific interactions among a subset of α-helical segments rather than a general hydrophobic collapse.
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Affiliation(s)
- Hossein Fazelinia
- Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, United States
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31
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Guca E, Roumestand C, Vallone B, Royer CA, Dellarole M. Low-cost equilibrium unfolding of heme proteins using 2 μl samples. Anal Biochem 2013; 443:13-5. [DOI: 10.1016/j.ab.2013.08.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/06/2013] [Accepted: 08/08/2013] [Indexed: 11/16/2022]
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32
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Liu J, Dong Y, Zheng J, He Y, Sheng Q. Investigation on the conformation change of hemoglobin immobilized on MPA-modified electrode by electrochemical method. ANAL SCI 2013; 29:1075-81. [PMID: 24212734 DOI: 10.2116/analsci.29.1075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The conformation change of bovine hemoglobin (Hb) during the unfolding process induced by urea and acid was investigated by an electrochemical method. Hb unfolding induced by urea of different concentrations was realized by bonding Hb onto a 3-mercaptopropionic acid (MPA) modified gold electrode. The difference in unfolding percentage showed that the Hb unfolding induced by urea was a two-step, three-state transition process, while the unfolding induced by acid was a two-state transition process. The results obtained by the electrochemical method coincided closely with those obtained by UV-vis spectroscopy and fluorescence spectroscopy. Some thermodynamic parameters during the conformational change were also calculated to study the intermediate state during the Hb unfolding process. The present work may lead to an easy and effective way to study metalloproteins unfolding, and holds great promise for the design of novel sensitive biosensors.
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Affiliation(s)
- Jianbo Liu
- Institute of Analytical Science/Shaanxi Provincial Key Laboratory of Electroanalytical Chemistry, Northwest University
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33
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Lee AJ, Asher WB, Stern HA, Bren KL, Krauss TD. Single-Molecule Analysis of Cytochrome c Folding by Monitoring the Lifetime of an Attached Fluorescent Probe. J Phys Chem Lett 2013; 4:2727-2733. [PMID: 24116268 PMCID: PMC3791595 DOI: 10.1021/jz401259y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Conformational dynamics of proteins are important for function. However, obtaining information about specific conformations is difficult for samples displaying heterogeneity. Here, time-resolved fluorescence resonance energy transfer is used to characterize the folding of single cytochrome c molecules. In particular, measurements of the fluorescence lifetimes of individual cytochrome c molecules labeled with a single dye that is quenched by energy transfer to the heme were used to monitor conformational transitions of the protein under partially denaturing conditions. These studies indicate significantly more conformational heterogeneity than has been described previously. Importantly, the use of a purified singly-labeled sample made a direct comparison to ensemble data possible. The distribution of lifetimes of single-proteins was compared to the distribution of lifetimes determined from analysis of ensemble lifetime fluorescence data. The results show broad agreement between single-molecule and ensemble data, with a similar range of lifetimes. However, the single-molecule data reveal greater conformational heterogeneity.
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34
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Sun Y, Karunakaran V, Champion PM. Investigations of the low-frequency spectral density of cytochrome c upon equilibrium unfolding. J Phys Chem B 2013; 117:9615-25. [PMID: 23863217 DOI: 10.1021/jp404881k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The equilibrium unfolding process of ferric horse heart cytochrome c (cyt c), induced by guanidinium hydrochloride (GdHCl), was studied using UV-vis absorption spectroscopy, resonance Raman spectroscopy, and vibrational coherence spectroscopy (VCS). The unfolding process was successfully fit using a three-state model which included the fully folded (N) and unfolded (U) states, along with an intermediate (I) assigned to a Lys bound heme. The VCS spectra revealed for the first time several low-frequency heme modes that are sensitive to cyt c unfolding: γ(a) (~50 cm(-1)), γ(b) (~80 cm(-1)), γ(c) (~100 cm(-1)), and ν(s)(His-Fe-His) at 205 cm(-1). These out-of-plane modes have potential functional relevance and are activated by protein-induced heme distortions. The free energies for the N-I and the I-U transitions at pH 7.0 and 20 °C were found to be 4.6 kcal/M and 11.6 kcal/M, respectively. Imidazole was also introduced to replace the methionine ligand so the unfolding can be modeled as a two-state system. The intensity of the mode γ(b)~80 cm(-1) remains nearly constant during the unfolding process, while the amplitudes of the other low frequency modes track with spectral changes observed at higher frequency. This confirms that the heme deformation changes are coupled to the protein tertiary structural changes that take place upon unfolding. These studies also reveal that damping of the coherent oscillations depends sensitively on the coupling between heme and the surrounding water solvent.
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Affiliation(s)
- Yuhan Sun
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, United States
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35
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Muenzner J, Toffey JR, Hong Y, Pletneva EV. Becoming a peroxidase: cardiolipin-induced unfolding of cytochrome c. J Phys Chem B 2013; 117:12878-86. [PMID: 23713573 DOI: 10.1021/jp402104r] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Interactions of cytochrome c (cyt c) with a unique mitochondrial glycerophospholipid cardiolipin (CL) are relevant for the protein's function in oxidative phosphorylation and apoptosis. Binding to CL-containing membranes promotes cyt c unfolding and dramatically enhances the protein's peroxidase activity, which is critical in early stages of apoptosis. We have employed a collection of seven dansyl variants of horse heart cyt c to probe the sequence of steps in this functional transformation. Kinetic measurements have unraveled four distinct processes during CL-induced cyt c unfolding: rapid protein binding to CL liposomes; rearrangements of protein substructures with small unfolding energies; partial insertion of the protein into the lipid bilayer; and extensive protein restructuring leading to "open" extended structures. While early rearrangements depend on a hierarchy of foldons in the native structure, the later process of large-scale unfolding is influenced by protein interactions with the membrane surface. The opening of the cyt c structure exposes the heme group, which enhances the protein's peroxidase activity and also frees the C-terminal helix to aid in the translocation of the protein through CL membranes.
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Affiliation(s)
- Julia Muenzner
- Department of Chemistry, Dartmouth College , Hanover, New Hampshire 03755, United States
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Varhač R. Urea-induced modification of cytochrome c flexibility as probed by cyanide binding. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:739-44. [DOI: 10.1016/j.bbapap.2013.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 01/08/2013] [Accepted: 01/09/2013] [Indexed: 11/25/2022]
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Dwivedi AK, Prasad KM, Trivedi V, Iyer PK. Interaction of heme proteins with anionic polyfluorene: insights into physiological effects, folding events, and inhibition activity. ACS APPLIED MATERIALS & INTERFACES 2012; 4:6371-6377. [PMID: 23113839 DOI: 10.1021/am302046n] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Because of the toxicity caused by the heme redox-active iron proteins, their elevated levels, localization, and accumulation in the brain, many forms of neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and Huntington's disease, occur as a result of which the brain becomes vulnerable to oxidative stress, ultimately resulting in neuronal death. An anionic water-soluble conjugated polyfluorene derivative poly(9,9-bis(6-sulfate hexyl) fluorene-alt-1,4-phenylene) sodium salt (P1) that binds Fe³⁺ proteins with very high selectivity and sensitivity is reported here. The photophysical properties of P1 were modified by the interaction with ferric heme-containing proteins cytochrome c (Cc), methemoglobin (MetHb), and hemin. P1 was found to be highly sensitive toward Fe³⁺ heme proteins as compared to nonmetalloproteins. We observed that the respective activities of ferric heme proteins were inhibited and proteins were unfolded, due to modification in their heme microenvironment in the presence of the polymer P1. The observations reported in this article provide the first example for the use of a water-soluble conjugated polymer in applications, such as (1) to detect small quantities of iron proteins in aqueous medium/physiological condition with the highest K(sv) values of 2.27 × 10⁸ M⁻¹ for Cc, 3.81 × 10⁷ M⁻¹ for MetHb, and 5.31 × 10⁷ M⁻¹ for hemin; (2) to study the physiological effects of heme metalloproteins; (3) to visualize the folding events in real time; and (4) the inhibition activity of metalloproteins can be selectively studied using a conjugated polymer based assay system rapidly without interference from nonmetalloproteins at biological pH. All this is achieved by generating optical events, taking advantage of the bright fluorescence of anionic polyfluorene P1 in this case, that can be observed and monitored by modification in the absorption and emission color in real time.
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Affiliation(s)
- Atul Kumar Dwivedi
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati-781039, India
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38
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Simon M, Metzinger-Le Meuth V, Chevance S, Delalande O, Bondon A. Versatility of non-native forms of human cytochrome c: pH and micellar concentration dependence. J Biol Inorg Chem 2012; 18:27-38. [DOI: 10.1007/s00775-012-0946-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 09/30/2012] [Indexed: 12/13/2022]
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Choi J, Fujitsuka M, Tojo S, Majima T. Folding Dynamics of Cytochrome c Using Pulse Radiolysis. J Am Chem Soc 2012; 134:13430-5. [DOI: 10.1021/ja304904p] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Jungkweon Choi
- The Institute of Scientific and
Industrial (SANKEN), Osaka University,
Mihogaoka 8-1, Ibaraki, Osaka 567-0047,
Japan
| | - Mamoru Fujitsuka
- The Institute of Scientific and
Industrial (SANKEN), Osaka University,
Mihogaoka 8-1, Ibaraki, Osaka 567-0047,
Japan
| | - Sachiko Tojo
- The Institute of Scientific and
Industrial (SANKEN), Osaka University,
Mihogaoka 8-1, Ibaraki, Osaka 567-0047,
Japan
| | - Tetsuro Majima
- The Institute of Scientific and
Industrial (SANKEN), Osaka University,
Mihogaoka 8-1, Ibaraki, Osaka 567-0047,
Japan
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40
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Xu M, Beresneva O, Rosario R, Roder H. Microsecond folding dynamics of apomyoglobin at acidic pH. J Phys Chem B 2012; 116:7014-25. [PMID: 22475221 DOI: 10.1021/jp3012365] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Apomyolgobin (apoMb) is an important model for understanding the folding mechanism of helical proteins. This study focuses on a partially structured state of sperm whale apoMb populated at pH 4.2 (M-state), which structurally resembles a late kinetic intermediate in the formation of the native state (N) at higher pH. The thermodynamics and cooperativity of apoMb folding at pH 4.2 and 6.2 were studied by global analysis of the urea-induced unfolding transitions monitored by tryptophan fluorescence and circular dichroism. The kinetics of folding and unfolding of apoMb at pH 4.2 was measured over a time window from 40 to 850 μs, using fluorescence-detected continuous-flow measurements. Our observation of biphasic kinetics provides clear evidence for rapid (<100 μs) accumulation of previously unresolved intermediate states in both refolding and unfolding experiments. Quantitative kinetic modeling of the results, using a four-state mechanism with two intermediates on a direct route between the unfolded and folded states (U↔I↔L↔M), gave new insight into the conformational states and barriers that precede the rate-limiting step in the formation of the N-state of apoMb.
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Affiliation(s)
- Ming Xu
- Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
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41
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Brunet C, Antoine R, Lemoine J, Dugourd P. Soret Band of the Gas-Phase Ferri-Cytochrome c. J Phys Chem Lett 2012; 3:698-702. [PMID: 26286275 DOI: 10.1021/jz300070r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We report the first visible spectrum of a heme-protein in the gas phase. The aim of this work was to provide a reference for the optical absorption of an isolated heme-protein to better understand the influence of protein conformation and fluctuation and of solvent on its optical properties. After laser irradiation of gas-phase cytochrome c (cyt c), electron emission is observed. Electron photodetachment yield of cyt c 6- was recorded in the region of the Soret band of the porphyrin group, showing a maximum at 410 nm. Our results are compared with optical spectra of gas-phase heme and of cyt c in solution. We discuss the influence of the polypeptide chain and of the solvent on both the position and the broadening of the Soret band. Action spectrum of gas-phase cyt c is close to the absorption of native cyt c in solution, suggesting an efficient protection of the heme group from solvent accessibility by the polypeptide chain and similar interactions between the two moieties in solution and the gas phase.
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Affiliation(s)
- Claire Brunet
- †Université Lyon 1, Lyon, France
- ‡CNRS, LASIM UMR 5579, 43 bd du 11 novembre 1918, 69622 Villeurbanne Cedex, France
- §CNRS, Institut des Sciences Analytique UMR 5180, 43 bd du 11 novembre 1918, 69622 Villeurbanne Cedex, France
| | - Rodolphe Antoine
- †Université Lyon 1, Lyon, France
- ‡CNRS, LASIM UMR 5579, 43 bd du 11 novembre 1918, 69622 Villeurbanne Cedex, France
| | - Jérôme Lemoine
- †Université Lyon 1, Lyon, France
- §CNRS, Institut des Sciences Analytique UMR 5180, 43 bd du 11 novembre 1918, 69622 Villeurbanne Cedex, France
| | - Philippe Dugourd
- †Université Lyon 1, Lyon, France
- ‡CNRS, LASIM UMR 5579, 43 bd du 11 novembre 1918, 69622 Villeurbanne Cedex, France
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42
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Patsalo V, Raleigh DP, Green DF. Rational and computational design of stabilized variants of cyanovirin-N that retain affinity and specificity for glycan ligands. Biochemistry 2011; 50:10698-712. [PMID: 22032696 PMCID: PMC3234137 DOI: 10.1021/bi201411c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Cyanovirin-N (CVN) is an 11 kDa pseudosymmetric cyanobacterial lectin that has been shown to inhibit infection by the human immunodeficiency virus by binding to high-mannose oligosaccharides on the surface of the viral envelope glycoprotein gp120. In this work, we describe rationally designed CVN variants that stabilize the protein fold while maintaining high affinity and selectivity for their glycan targets. Poisson-Boltzmann calculations and protein repacking algorithms were used to select stabilizing mutations in the protein core. By substituting the buried polar side chains of Ser11, Ser20, and Thr61 with aliphatic groups, we stabilized CVN by nearly 12 °C against thermal denaturation, and by 1 M GuaHCl against chemical denaturation, relative to a previously characterized stabilized mutant. Glycan microarray binding experiments confirmed that the specificity profile of carbohydrate binding is unperturbed by the mutations and is identical for all variants. In particular, the variants selectively bound glycans containing the Manα(1→2)Man linkage, which is the known minimal binding unit of CVN. We also report the slow denaturation kinetics of CVN and show that they can complicate thermodynamic analysis; in particular, the unfolding of CVN cannot be described as a fixed two-state transition. Accurate thermodynamic parameters are needed to describe the complicated free energy landscape of CVN, and we provide updated values for CVN unfolding.
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Affiliation(s)
- Vadim Patsalo
- Department of Applied Mathematics and Statistics Stony Brook University Stony Brook, New York 11794 USA
- Laufer Center for Physical and Quantitative Biology Stony Brook University Stony Brook, New York 11794 USA
| | - Daniel P. Raleigh
- Department of Chemistry Stony Brook University Stony Brook, New York 11794 USA
- Graduate Program in Biochemistry and Structural Biology Stony Brook University Stony Brook, New York 11794 USA
| | - David F. Green
- Department of Applied Mathematics and Statistics Stony Brook University Stony Brook, New York 11794 USA
- Laufer Center for Physical and Quantitative Biology Stony Brook University Stony Brook, New York 11794 USA
- Department of Chemistry Stony Brook University Stony Brook, New York 11794 USA
- Graduate Program in Biochemistry and Structural Biology Stony Brook University Stony Brook, New York 11794 USA
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Ahluwalia U, Prakash C, Agrawal R, Deep S. Characterization of cytochrome c folding intermediates induced by sucrose and phosphate. Int J Biol Macromol 2011; 49:752-60. [DOI: 10.1016/j.ijbiomac.2011.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 07/09/2011] [Accepted: 07/11/2011] [Indexed: 10/17/2022]
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44
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Side-chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers. Proc Natl Acad Sci U S A 2011; 108:10174-7. [PMID: 21606332 DOI: 10.1073/pnas.1103979108] [Citation(s) in RCA: 232] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The transfer free energies of the twenty natural amino acid side chains from water to phospholipid bilayers make a major contribution to the assembly and function of membrane proteins. Measurements of those transfer free energies will facilitate the identification of membrane protein sequences and aid in the understanding of how proteins interact with membranes during key biological events. We report the first water-to-bilayer transfer free energy scale (i.e., a "hydrophobicity scale") for the twenty natural amino acid side chains measured in the context of a native transmembrane protein and a phospholipid bilayer. Our measurements reveal parity for apolar side-chain contributions between soluble and membrane proteins and further demonstrate that an arginine side-chain placed near the middle of a lipid bilayer is accommodated with much less energetic cost than predicted by molecular dynamics simulations.
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45
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Bian L, Zhang T, Yang X, Liu L, Zheng X. Unfolding of Bovine Heart Cytochrome c Induced by Urea and Guanidine Hydrochloride. CHINESE J CHEM 2011. [DOI: 10.1002/cjoc.201190163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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46
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Nakamura S, Seki Y, Katoh E, Kidokoro SI. Thermodynamic and structural properties of the acid molten globule state of horse cytochrome C. Biochemistry 2011; 50:3116-26. [PMID: 21388230 DOI: 10.1021/bi101806b] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To understand the stabilization, folding, and functional mechanisms of proteins, it is very important to understand the structural and thermodynamic properties of the molten globule state. In this study, the global structure of the acid molten globule state, which we call MG1, of horse cytochrome c at low pH and high salt concentrations was evaluated by solution X-ray scattering (SXS), dynamic light scattering, and circular dichroism measurements. MG1 was globular and slightly (3%) larger than the native state, N. Calorimetric methods, such as differential scanning calorimetry and isothermal acid-titration calorimetry, were used to evaluate the thermodynamic parameters in the transitions of N to MG1 and MG1 to denatured state D of horse cytochrome c. The heat capacity change, ΔC(p), in the N-to-MG1 transition was determined to be 2.56 kJ K(-1) mol(-1), indicating the increase in the level of hydration in the MG1 state. Moreover, the intermediate state on the thermal N-to-D transition of horse cytochrome c at pH 4 under low-salt conditions showed the same structural and thermodynamic properties of the MG1 state in both SXS and calorimetric measurements. The Gibbs free energy changes (ΔG) for the N-to-MG1 and N-to-D transitions at 15 °C were 10.9 and 42.2 kJ mol(-1), respectively.
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Affiliation(s)
- Shigeyoshi Nakamura
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
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47
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Khan MKA, Rahaman H, Ahmad F. Conformation and thermodynamic stability of pre-molten and molten globule states of mammalian cytochromes-c. Metallomics 2011; 3:327-38. [DOI: 10.1039/c0mt00078g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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48
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Bischin C, Deac F, Silaghi-Dumitrescu R, Worrall JAR, Rajagopal BS, Damian G, Cooper CE. Ascorbate peroxidase activity of cytochrome c. Free Radic Res 2010; 45:439-44. [PMID: 21128733 DOI: 10.3109/10715762.2010.540575] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The peroxidase-type reactivity of cytochrome c is proposed to play a role in free radical production and/or apoptosis. This study describes cytochrome c catalysis of peroxide consumption by ascorbate. Under conditions where the sixth coordination position at the cytochrome c heme iron becomes more accessible for exogenous ligands (by carboxymethylation, cardiolipin addition or by partial denaturation with guanidinium hydrochloride) this peroxidase activity is enhanced. A reaction intermediate is detected by stopped-flow UV-vis spectroscopy upon reaction of guanidine-treated cytochrome c with peroxide, which resembles the spectrum of globin Compound II species and is thus proposed to be a ferryl species. The ability of physiological levels of ascorbate (10-60 µM) to interact with this species may have implications for mechanisms of cell signalling or damage that are based on cytochrome c/peroxide interactions.
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Affiliation(s)
- Cristina Bischin
- Department of Chemistry and Chemical Engineering, 'Babes-Bolyai' University, Cluj-Napoca RO-400028, Romania.
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Haldar S, Mitra S, Chattopadhyay K. Role of protein stabilizers on the conformation of the unfolded state of cytochrome c and its early folding kinetics: investigation at single molecular resolution. J Biol Chem 2010; 285:25314-23. [PMID: 20538585 PMCID: PMC2919094 DOI: 10.1074/jbc.m110.116673] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2010] [Revised: 05/31/2010] [Indexed: 11/06/2022] Open
Abstract
An insight into the conformation and dynamics of unfolded and early intermediate states of a protein is essential to understand the mechanism of its aggregation and to design potent inhibitor molecules. Fluorescence correlation spectroscopy has been used to study the effects of several model protein stabilizers on the conformation of the unfolded state and early folding dynamics of tetramethyl rhodamine-labeled cytochrome c from Saccharomyces cerevisiae at single molecular resolution. Special attention has been given to arginine, which is a widely used stabilizer for improving refolding yield of different proteins. The value of the hydrodynamic radius (r(H)) obtained by analyzing the intensity fluctuations of the diffusing molecules has been found to increase in a two-state manner as the protein is unfolded by urea. The results further show that the presence of arginine and other protein stabilizers favors a relatively structured conformation of the unfolded states (r(H) of 29 A) over an extended one (r(H) of 40 A), which forms in their absence. Also, the time constant of a kinetic component (tau(R)) of about 30 micros has been observed by analyzing the correlation functions, which represents formation of a collapsed state. This time constant varies with urea concentration representing an inverted Chevron plot that shows a roll-over and behavior in the absence of arginine. To the best of our knowledge, this is one of the first applications of fluorescence correlation spectroscopy to study direct folding kinetics of a protein.
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Affiliation(s)
- Shubhasis Haldar
- From the Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Samaresh Mitra
- From the Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Krishnananda Chattopadhyay
- From the Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S. C. Mullick Road, Kolkata 700032, India
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50
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Conformational and thermodynamic characterization of the premolten globule state occurring during unfolding of the molten globule state of cytochrome c. J Biol Inorg Chem 2010; 15:1319-29. [DOI: 10.1007/s00775-010-0691-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 07/20/2010] [Indexed: 10/19/2022]
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