1
|
Hossain M, Huda N, Bhuyan AK. A three-state mechanism for trifluoroethanol denaturation of an intrinsically disordered protein (IDP). J Biochem 2023; 174:519-531. [PMID: 37709541 DOI: 10.1093/jb/mvad067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 09/16/2023] Open
Abstract
Relating the amino acid composition and sequence to chain folding and binding preferences of intrinsically disordered proteins (IDPs) has emerged as a huge challenge. While globular proteins have respective 3D structures that are unique to their individual functions, IDPs violate this structure-function paradigm because rather than having a well-defined structure an ensemble of rapidly interconverting disordered structures characterize an IDP. This work measures 2,2,2-trifluoroethanol (TFE)-induced equilibrium transitions of an IDP called AtPP16-1 (Arabidopsis thaliana phloem protein type 16-1) by using fluorescence, circular dichroism, infrared and nuclear magnetic resonance (NMR) methods at pH 4, 298 K. Low TFE reversibly removes the tertiary structure to produce an ensemble of obligate intermediate ($\mathrm{I}$) retaining the native-state ($\mathrm{N}$) secondary structure. The intermediate $\mathrm{I}$ is preceded by a non-obligate tryptophan-specific intermediate ${\mathrm{I}}_{\mathrm{w}}$ whose population is detectable for AtPP16-1 specifically. Accumulation of such non-obligate intermediates is discriminated according to the sequence composition of the protein. In all cases, however, a tertiary structure-unfolded general obligate intermediate $\mathrm{I}$ is indispensable. The $\mathrm{I}$ ensemble has higher helical propensity conducive to the acquisition of an exceedingly large level of α-helices by a reversible denaturation transition of $\mathrm{I}$ to the denatured state $\mathrm{D}$ as the TFE level is increased. Strikingly, it is the same $\mathrm{N}\rightleftharpoons \mathrm{I}\rightleftharpoons \mathrm{D}$ scheme typifying the TFE transitions of globular proteins. The high-energy state $\mathrm{I}$ characterized by increased helical propensity is called a universal intermediate encountered in both genera of globular and disordered proteins. Neither $\mathrm{I}$ nor $\mathrm{D}$ strictly show molten globule (MG)-like properties, dismissing the belief that TFE promotes MGs.
Collapse
Affiliation(s)
- Mujahid Hossain
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Noorul Huda
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Abani K Bhuyan
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| |
Collapse
|
2
|
Gazi R, Maity S, Jana M. Conformational Features and Hydration Dynamics of Proteins in Cosolvents: A Perspective from Computational Approaches. ACS OMEGA 2023; 8:2832-2843. [PMID: 36713749 PMCID: PMC9878537 DOI: 10.1021/acsomega.2c08009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
The importance of solvent in stabilizing protein structures has long been recognized. Water is the common solvent for proteins, and hydration is elemental in governing protein stability, flexibility, and function through various interactions. The addition of small organic molecules known as cosolvents may deploy stabilization (folding) or destabilization (unfolding) effects on native protein conformations. Despite exhaustive literature, the molecular mechanism by which cosolvents regulate protein conformations and dynamics is controversial. Specifically, the cosolvent behavior has been unpredictable with the nature and concentrations that lead to protein stabilizing/destabilizing effects as it changes in water content near the vicinity of proteins. With the massive development of computational resources, advancement of computational methods, and the availability of numerous experimental techniques, various theoretical and computational studies of proteins in a mixture of solvents have been instigated. The growing interest in such studies has been to unravel the underlying mechanism of protein folding and cosolvent/solvent-protein interactions that have significant implications in biomedical and biotechnological applications. In this mini-review, apart from the brief overview of important theories and force-field model-based cosolvent effects on proteins, we present the current state of knowledge and recent advances in the field to describe cosolvent-guided conformational features of proteins and hydration dynamics from computational approaches. The mini-review further explains the mechanistic details of protein stability in various popularly used cosolvents, including limitations of present studies and future outlooks. The counteracting effects of cosolvent on the proteins in the mixture of stabilizing and destabilizing cosolvents are also presented and discussed.
Collapse
|
3
|
Hossain M, Huda N, Bhuyan AK. A surprisingly simple three-state generic process for reversible protein denaturation by trifluoroethanol. Biophys Chem 2022; 291:106895. [PMID: 36182744 DOI: 10.1016/j.bpc.2022.106895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 12/30/2022]
Abstract
Despite the rich knowledge of the influence of 2,2,2-trifluoroethanol (TFE) on the structure and conformation of peptides and proteins, the mode(s) of TFE-protein interactions and the mechanism by which TFE reversibly denatures a globular protein remain elusive. This study systematically examines TFE-induced equilibrium transition curves for six paradigmatic globular proteins by using basic fluorescence and circular dichroism measurements under neutral pH conditions. The results are remarkably simple. Low TFE invariably unfolds the tertiary structure of all proteins to produce the obligate intermediate (I) which retains nearly all of native-state secondary structure, but enables the formation of extra α-helices as the level of TFE is raised higher. Inspection of the transitions at once reveals that the tertiary structure unfolding is always a distinct process, necessitating the inclusion of at least one obligate intermediate in the TFE-induced protein denaturation. It appears that the intermediate in the minimal unfolding mechanism N⇌I⇌D somehow acquires higher α-helical propensity to generate α-helices in excess of that in the native state to produce the denatured state (D), also called the TFE state. The low TFE-populated intermediate I may be called a universal intermediate by virtue of its α-helical propensity. Contrary to many earlier suggestions, this study dismisses molten globule (MG)-like attribute of I or D.
Collapse
Affiliation(s)
- Mujahid Hossain
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Noorul Huda
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Abani K Bhuyan
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India.
| |
Collapse
|
4
|
Pyne P, Das Mahanta D, Gohil H, Prabhu SS, Mitra RK. Correlating solvation with conformational pathways of proteins in alcohol-water mixtures: a THz spectroscopic insight. Phys Chem Chem Phys 2021; 23:17536-17544. [PMID: 34369530 DOI: 10.1039/d1cp01841h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Water, being an active participant in most of the biophysical processes, is important to trace how protein solvation changes as its conformation evolves in the presence of solutes or co-solvents. In this study, we investigate how the secondary structures of two diverse proteins - lysozyme and β-lactoglobulin - change in the aqueous mixtures of two alcohols - ethanol and 2,2,2-trifluoroethanol (TFE) using circular dichroism measurements. We observe that these alcohols change the secondary structures of these proteins and the changes are protein-specific. Subsequently, we measure the collective solvation dynamics of these two proteins both in the absence and in the presence of alcohols by measuring the frequency-dependent absorption coefficient (α(ν)) in the THz (0.1-1.2 THz) frequency domain. The alcohol-water mixtures exhibit a non-ideal behaviour with the highest absorption difference (Δα) obtained at Xalcohol = 0.2. The protein solvation in the presence of the alcohols shows an oscillating behaviour in which Δαprotein changes with Xalcohol. Such an oscillatory behaviour of protein solvation results from a delicate interplay between the protein-water, protein-alcohol and water-alcohol associations. We attempt to correlate the various structural conformations of the proteins with the associated solvation.
Collapse
Affiliation(s)
- Partha Pyne
- Department of Chemical, Biological & Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences, Block-JD; Sector-III; Salt Lake, Kolkata-700106, India.
| | | | | | | | | |
Collapse
|
5
|
Ohgi H, Imamura H, Sumi T, Nishikawa K, Koga Y, Westh P, Morita T. Two different regimes in alcohol-induced coil-helix transition: effects of 2,2,2-trifluoroethanol on proteins being either independent of or enhanced by solvent structural fluctuations. Phys Chem Chem Phys 2021; 23:5760-5772. [PMID: 33481971 DOI: 10.1039/d0cp05103a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Inhomogeneous distribution of constituent molecules in a mixed solvent has been known to give remarkable effects on the solute, e.g., conformational changes of biomolecules in an alcohol-water mixture. We investigated the general effects of 2,2,2-trifluoroethanol (TFE) on proteins/peptides in a mixture of water and TFE using melittin as a model protein. Fluctuations and Kirkwood-Buff integrals (KBIs) in the TFE-H2O mixture, quantitative descriptions of inhomogeneity, were determined by small-angle X-ray scattering investigation and compared with those in the aqueous solutions of other alcohols. The concentration fluctuation for the mixtures ranks as methanol < ethanol ≪ TFE < tert-butanol < 1-propanol, indicating that the inhomogeneity of molecular distribution in the TFE-H2O mixture is unexpectedly comparable to those in the series of mono-ols. On the basis of the concentration dependence of KBIs between the TFE molecules, it was found that a strong attraction between the TFE molecules is not necessarily important to induce helix conformation, which is inconsistent with the previously proposed mechanism. To address this issue, by combining the KBIs and the helix contents reported by the experimental spectroscopic studies, we quantitatively evaluated the change in the preferential binding parameter of TFE to melittin attributed to the coil-helix transition. As a result, we found two different regimes on TFE-induced helix formation. In the dilute concentration region of TFE below ∼2 M, where the TFE molecules are not aggregated among themselves, the excess preferential binding of TFE to the helix occurs due to the direct interaction between them, namely independent of the solvent fluctuation. In the higher concentration region above ∼2 M, in addition to the former effect, the excess preferential binding is significantly enhanced by the solvent fluctuation. This scheme should be held as general cosolvent effects of TFE on proteins/peptides.
Collapse
Affiliation(s)
- Hiroyo Ohgi
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan.
| | - Hiroshi Imamura
- Department of Applied Chemistry, College of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Tomonari Sumi
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan.
| | - Keiko Nishikawa
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan. and Toyota Physical & Chemical Research Institute, Nagakute, Aichi 480-1192, Japan
| | - Yoshikata Koga
- Department of Chemistry, The University of British Columbia, Vancouver, V6T 1Z1, Canada
| | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800, Kgs, Lyngby, Denmark
| | - Takeshi Morita
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan.
| |
Collapse
|
6
|
He L, Ying L, Jingting X, Chen C, Shuntang G. Changes in the secondary structures and zeta potential of soybean peptide and its calcium complexes in different solution environments. Food Funct 2021; 12:5967-5974. [PMID: 34032239 DOI: 10.1039/d0fo03478a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
To illustrate the relationship between environment hydrophobicity and soybean peptide and its calcium complexes when they are absorbed transmembrane, different solution environments (HBS buffer, TFE hydrophobic solution and cell suspension) were used to simulate hydrophilic and hydrophobic environments. In this study, soybean peptides (10-30 kDa) with a high calcium binding capacity were prepared by enzymatic hydrolysis and ultrafiltration. The results of cell experiments showed that the peptide could transport calcium into cells for absorption. Secondary structure changes of the peptide and its calcium complexes in different solution environments showed that the secondary structure of the peptide changed during the transmembrane absorption, and the contents of α-helix and β-sheet structures increased. Besides, the β-sheet structures in the peptide-calcium complexes were further converted to an α-helix structure. This conversion may be induced by the hydrophobicity of peptide solutions. In addition, when the conformation changes, the positively charged peptides in the sample will be exposed and then interact with cells, which is beneficial for the transmembrane of peptide-calcium complexes.
Collapse
Affiliation(s)
- Liu He
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China. and Yunnan Urban Agricultural Engineering and Technological Research Center, College of Agriculture and Life Sciences, Kunming University, Kunming, 650214, China
| | - Lv Ying
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China. and Department of Food Science, Beijing University of Agriculture, Beijing, 102206, China
| | - Xu Jingting
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
| | - Chen Chen
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
| | - Guo Shuntang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
| |
Collapse
|
7
|
Santra S, Dhurua S, Jana M. Analyzing the driving forces of insulin stability in the basic amino acid solutions: A perspective from hydration dynamics. J Chem Phys 2021; 154:084901. [PMID: 33639734 DOI: 10.1063/5.0038305] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Amino acids having basic side chains, as additives, are known to increase the stability of native-folded state of proteins, but their relative efficiency and the molecular mechanism are still controversial and obscure as well. In the present work, extensive atomistic molecular dynamics simulations were performed to investigate the hydration properties of aqueous solutions of concentrated arginine, histidine, and lysine and their comparative efficiency on regulating the conformational stability of the insulin monomer. We identified that in the aqueous solutions of the free amino acids, the nonuniform relaxation of amino acid-water hydrogen bonds was due to the entrapment of water molecules within the amino acid clusters formed in solutions. Insulin, when tested with these solutions, was found to show rigid conformations, relative to that in pure water. We observed that while the salt bridges formed by the lysine as an additive contributed more toward the direct interactions with insulin, the cation-π was more prominent for the insulin-arginine interactions. Importantly, it was observed that the preferentially more excluded arginine, compared to histidine and lysine from the insulin surface, enriches the hydration layer of the protein. Our study reveals that the loss of configurational entropy of insulin in arginine solution, as compared to that in pure water, is more as compared to the entropy loss in the other two amino acid solutions, which, moreover, was found to be due to the presence of motionally bound less entropic hydration water of insulin in arginine solution than in histidine or lysine solution.
Collapse
Affiliation(s)
- Santanu Santra
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
| | - Shakuntala Dhurua
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
| | - Madhurima Jana
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
| |
Collapse
|
8
|
Exploring the effect of hydrogen bonding on protonation of 7,8-benzoquinoline with TFE: Water binary mixture. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
9
|
Abstract
There is an opinion in professional literature that edge-strands in β-sheet are critical to the processes of amyloid transformation. Propagation of fibrillar forms mainly takes place on the basis of β-sheet type interactions. In many proteins, the edge strands represent only a partially matched form to the β-sheet. Therefore, the edge-strand takes slightly distorted forms. The assessment of the level of arrangement can be carried out based on studying the secondary structure as well as the structure of the hydrophobic core. For this purpose, a fuzzy oil drop model was used to determine the contribution of each fragment with a specific secondary structure to the construction of the system being the effect of a certain synergy, which results in the construction of a hydrophobic core. Studying the participation of β-sheets edge fragments in the hydrophobic core construction is the subject of the current analysis. Statuses of these edge fragments in β-sheets in ferredoxin-like folds are treated as factors that disturb the symmetry of the system.
Collapse
|
10
|
Lacson CFZ, Lu MC, Huang YH. Fluoride network and circular economy as potential model for sustainable development-A review. CHEMOSPHERE 2020; 239:124662. [PMID: 31499305 DOI: 10.1016/j.chemosphere.2019.124662] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/13/2019] [Accepted: 08/23/2019] [Indexed: 06/10/2023]
Abstract
Fluorine is the most reactive elements among the halogen group and commonly and ubiquitously occurs as fluoride in nature. The industrial processes produce fluoride by-products causing the increase of unwanted environmental levels and consequently posing risk on human and environmental health worldwide. This review gives a fundamental understanding of fluoride networks in the industrial processes, in the geological and hydrological transport, and in the biological sphere. Numerous biological pathways of fluoride also increase the risk of exposure. Literature shows that various environmental levels of fluoride due to its chemical characteristics cause bioaccumulation resulting in health deterioration among organisms. These problems are aggravated by emitted fluoride in the air and wastewater streams. Moreover, the current waste disposal dependent on incineration and landfilling superpose to the problem. In our analysis, the fluoride material flow model still follows a linear economy and reuse economy to some extent. This flow model spoils resources with high economic potential and worsens environmental problems. Thus, we intend a shift from the conventional linear economy to a circular economy with the revival of three-dimensional objectives of sustainable development. Linkages between key dimensions of the circular economy to stimulate momentum for perpetual sustainable development are proposed to gain economic, environmental and social benefits.
Collapse
Affiliation(s)
- Carl Francis Z Lacson
- Department of Chemical Engineering, Sustainable Environment Research Center, National Cheng Kung University, Tainan, 701, Taiwan
| | - Ming-Chun Lu
- Department of Environmental Resources Management, Chia Nan University of Pharmacy and Science, Tainan, 71710, Taiwan.
| | - Yao-Hui Huang
- Department of Chemical Engineering, Sustainable Environment Research Center, National Cheng Kung University, Tainan, 701, Taiwan.
| |
Collapse
|
11
|
Abstract
A sizeable proportion of active protein sequences lack structural motifs making them irresolvable by NMR and crystallography. Such intrinsically disordered proteins (IDPs) or regions (IDRs) play a major role in biological mechanisms. They are often involved in cell regulation processes, and by extension can be the perpetrator or signifier of disease. In light of their importance and the shortcomings of conventional methods of biophysical analysis to identify them and to describe their conformational variance, IDPs and IDRs have been termed "the dark proteome." In this chapter we describe the use of ion mobility-mass spectrometry (IM-MS) coupled with electrospray ionization to analyze the conformational diversity of IDPs. Using the LEA protein COR15A as an exemplar system and contrasting it with the behavior of myoglobin, we outline the methods for analyzing an IDP using nanoelectrospray ionization coupled with IM-MS, covering sample preparation, purification; optimization of mass spectrometry conditions and tuning parameters; data collection and analysis. Following this, we detail the use of a "toy" model that provides a predictive framework for the study of all proteins with ESI-IM-MS.
Collapse
|