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Sadarangani V, Kalia A, Kausar T, Murarka P, Sau AK. Effect of the Macromolecular Crowding Agents on the Structure and Function of Human Arginase-I, a Therapeutically Important Enzyme. J Phys Chem B 2023; 127:8749-8761. [PMID: 37796726 DOI: 10.1021/acs.jpcb.3c02940] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Macromolecular crowding has been known to influence the structure and function of many enzymes through excluded volume effects and/or soft interactions. Here, we employed two synthetic macromolecular crowders, Dextrans and poly(ethylene glycol)s (PEGs) with varying molecular masses, to examine how they affected the structure and function of a therapeutically important enzyme, human arginase-I that catalyzes the conversion of l-arginine to l-ornithine and urea. Except at greater concentrations of Dextran 200, Dextrans were observed to slightly reduce the enzymatic activity, indicating that they exert their influence mainly through the excluded volume effects. Similar outcomes were seen with PEGs, with the exception of PEG 1000, where the activity decreased with increasing PEG concentrations, showing the maximum effect at a 20 g/L concentration. This finding suggests that the enzyme function is reduced by the soft interactions of this macromolecule with the enzyme, supported by the binding measurement. Secondary and local tertiary structures and thermodynamic stability were also affected, suggesting that PEG 1000 has an impact on the protein's structure. Furthermore, molecular dynamics simulation studies suggest that the catalytic pocket is disturbed, presumably by the unwinding of neighboring helix 9. As a result, the positioning of nearby Glu277 is altered, which prevents His141 and Glu277 from making contact. This hampers the proton transfer from the catalytic His141 to the intermediate species to form ornithine, a crucial step for the substrate hydrolysis reaction by this arginase. Overall, the knowledge gained from this study might be helpful for understanding how different enzymes work in a crowded/cellular environment.
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Affiliation(s)
- Vineet Sadarangani
- Protein Engineering Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Anjali Kalia
- Protein Engineering Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Tasneem Kausar
- Protein Engineering Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Pooja Murarka
- Protein Engineering Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Apurba Kumar Sau
- Protein Engineering Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
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2
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Dai J, Peng Z, Shen S, Huang B, Ren L, Liu J, Chen CH, Chen G. Evaluation of exogenous therapeutic protein activity under confinement and crowding effects. NANOSCALE 2023; 15:13450-13458. [PMID: 37548227 DOI: 10.1039/d3nr02968a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Dysfunction of intracellular proteins is frequently associated with various diseases, such as cancer. The exogenous proteins in cells are usually assembled with specific configurations due to physiological confinement/crowding to exhibit novel features in the protein structure, folding or conformational stability, distinguished with their behaviors in buffer solutions. Here, we synthesized exogenous proteins under confined/crowded conditions, to explore protein activity within cells. The findings suggested that the confinement and crowding effects on protein activity are heterogeneous; they showed an inhibitory effect on HRP by decreasing Km from ∼9.5- and ∼21.7-fold and Vmax from ∼6.8- and ∼20.2-fold lower than that of dilute solutions. Interestingly, the effects on Cyt C seem to be more complicated, and crowding exerts a positive effect by increasing Km ∼ 3.6-fold and Vmax ∼ 1.5-fold higher than that of dilute solutions; however, confinement exhibits a negative effect by decreasing Km ∼2.0 and Vmax ∼8.3 times. Additionally, in contrast to traditional nanoparticle-based confinement models, we synthesized a biodegradable nanoparticle to mimic the confined space, and the biggest advantage of this novel model is that the particles can be degraded and thus it can provide more intuitive observations of the properties of the target proteins under confinement and after release. Furthermore, we also evaluated protein activity in different cellular environments, indicating that the exogenous protein activity was closely related to the crowdedness of cellular environments, and the inhibition of protein activity in MDA-MB-231 cancer cells was more obvious than in HEK293 normal cells. Finally, SAXS analysis revealed the correlation between the protein conformation and the different environments. Our work will provide a unique method for precisely assessing whether the target cellular environments are native matrix in which specific exogenous protein drugs are delivered to function or whether they display a therapeutic role, which is of great significance for screening and development of new drugs.
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Affiliation(s)
- Jie Dai
- School of Pharmaceutical Sciences, Nanjing Tech University, 30th Puzhu South Road, Nanjing 211816, China.
| | - Zhiyi Peng
- School of Pharmaceutical Sciences, Nanjing Tech University, 30th Puzhu South Road, Nanjing 211816, China.
| | - Shuwei Shen
- School of Pharmaceutical Sciences, Nanjing Tech University, 30th Puzhu South Road, Nanjing 211816, China.
| | - Binbin Huang
- School of Pharmaceutical Sciences, Nanjing Tech University, 30th Puzhu South Road, Nanjing 211816, China.
| | - Lili Ren
- School of Pharmaceutical Sciences, Nanjing Tech University, 30th Puzhu South Road, Nanjing 211816, China.
| | - Jia Liu
- School of Pharmaceutical Sciences, Nanjing Tech University, 30th Puzhu South Road, Nanjing 211816, China.
| | - Chia-Hung Chen
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China.
| | - Guoguang Chen
- School of Pharmaceutical Sciences, Nanjing Tech University, 30th Puzhu South Road, Nanjing 211816, China.
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3
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Connecting the Dots: Macromolecular Crowding and Protein Aggregation. J Fluoresc 2023; 33:1-11. [PMID: 36417150 DOI: 10.1007/s10895-022-03082-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/09/2022] [Indexed: 11/24/2022]
Abstract
Proteins are one of the dynamic macromolecules that play a significant role in many physiologically important processes to sustain life on the earth. Proteins need to be properly folded into their active conformation to perform their function. Alteration in the protein folding process may lead to the formation of misfolded conformers. Accumulation of these misfolded conformers can result in the formation of protein aggregates which are attributed to many human pathological conditions including neurodegeneration, cataract, neuromuscular disorders, and diabetes. Living cells naturally have heterogeneous crowding environments with different concentrations of various biomolecules. Macromolecular crowding condition has been found to alter the protein conformation. Here in this review, we tried to show the relation between macromolecular crowding, protein aggregation, and its consequences.
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4
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Interaction of Thioflavin T (ThT) and 8-anilino-1-naphthalene sulfonic acid (ANS) with macromolecular crowding agents and their monomers: Biophysical analysis using in vitro and computational approaches. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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5
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Mondal S, Das S, Swamy MJ. Macromolecular Crowding Significantly Affects the Conformational Features and Carbohydrate Binding Properties of CIA17, a PP2-Type Lectin from Coccinia indica. Biochemistry 2022; 61:2344-2357. [PMID: 36200563 DOI: 10.1021/acs.biochem.2c00389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effect of macromolecular crowding on the conformational features and carbohydrate binding properties of CIA17, a PP2-type lectin, was investigated employing polymeric dextrans D6, D40, and D70 (Mr ∼ 6, 40, and 70 kDa, respectively) as crowders. While the secondary structure of CIA17 was significantly affected by D6, with a considerable decrease in the number of β-sheets and β-turns with a corresponding increase in the number of unordered structures, relatively smaller changes were induced by D40 and D70. However, differential scanning calorimetry (DSC) studies revealed that the thermal stability of the protein remains unchanged in the presence of crowders. While the larger dextrans, D70 and D40, induced modest quenching (∼10%) of the protein fluorescence by a static pathway, the smaller D6 induced a higher degree of quenching (37%), which involved both static and collisional quenching processes. The results of fluorescence correlation spectroscopy measurements together with DSC studies suggested that CIA17 forms larger oligomers in the presence of D40 and D70 but D6 prevents the formation of higher-order oligomers. The association constant for the CIA17-chitooligosaccharide interaction increased by ∼30% and 160% in the presence of D40 and D70, respectively, but decreased by ∼30% in the presence of D6. The higher binding affinity can be attributed to the excluded volume effect, i.e., an increased effective concentration of the protein in the presence of D40 and D70, whereas D6, being smaller, possibly penetrates into the protein interior, disrupting the water structure around the protein and also inducing conformational changes, resulting in weaker binding. These observations demonstrate that molecular crowding significantly affects the carbohydrate binding characteristics of lectins, which can modulate their physiological function.
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Affiliation(s)
- Saradamoni Mondal
- School of Chemistry, University of Hyderabad, Hyderabad500 046, India
| | - Somnath Das
- School of Chemistry, University of Hyderabad, Hyderabad500 046, India
| | - Musti J Swamy
- School of Chemistry, University of Hyderabad, Hyderabad500 046, India
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6
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Irukuvajjula SS, Reddy JG, Vadrevu R. Crowding by Poly(ethylene glycol) Destabilizes Chemotaxis Protein Y (CheY). Biochemistry 2022; 61:1431-1443. [PMID: 35796609 DOI: 10.1021/acs.biochem.2c00030] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The prevailing understanding of various aspects of biochemical processes, including folding, stability, intermolecular interactions, and the binding of metals, substrates, and inhibitors, is derived from studies carried out under dilute and homogeneous conditions devoid of a crowding-related environment. The effect of crowding-induced modulation on the structure and stability of native and magnesium-dependent Chemotaxis Y (CheY), a bacterial signaling protein, was probed in the presence and absence of poly(ethylene glycol) (PEG). A combined analysis from circular dichroism, intrinsic and extrinsic fluorescence, and tryptophan fluorescence lifetime changes indicates that PEG perturbs the structure but leaves the thermal stability largely unchanged. Intriguingly, while the stability of the protein is enhanced in the presence of magnesium under dilute buffer conditions, PEG-induced crowding leads to reduced thermal stability in the presence of magnesium. Nuclear magnetic resonance (NMR) chemical shift perturbations and resonance broadening for a subset of residues indicate that PEG interacts specifically with a subset of hydrophilic and hydrophobic residues found predominantly in α helices, β strands, and in the vicinity of the metal-binding region. Thus, PEG prompted conformational perturbation, presumably provides a different situation for magnesium interaction, thereby perturbing the magnesium-prompted stability. In summary, our results highlight the dominance of enthalpic contributions between PEG and CheY via both hydrophilic and hydrophobic interactions, which can subtly affect the conformation, modulating the metal-protein interaction and stability, implying that in the context of cellular situation, structure, stability, and magnesium binding thermodynamics of CheY may be different from those measured in dilute solution.
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Affiliation(s)
- Shivkumar Sharma Irukuvajjula
- Department of Biological Sciences, Birla Institute of Technology & Science─Pilani, Hyderabad Campus, Jawahar Nagar, Shamirpet, Hyderabad 500078, India
| | - Jithender G Reddy
- NMR Division, Department of Analytical & Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Ministry of Science and Technology, Uppal Road, Tarnaka, Hyderabad 500007, India
| | - Ramakrishna Vadrevu
- Department of Biological Sciences, Birla Institute of Technology & Science─Pilani, Hyderabad Campus, Jawahar Nagar, Shamirpet, Hyderabad 500078, India
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7
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Bazmi S, Wallin S. Crowding-induced protein destabilization in the absence of soft attractions. Biophys J 2022; 121:2503-2513. [PMID: 35672949 DOI: 10.1016/j.bpj.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 04/18/2022] [Accepted: 06/01/2022] [Indexed: 11/02/2022] Open
Abstract
It is generally assumed that volume exclusion by macromolecular crowders universally stabilizes the native states of proteins and destabilization suggests soft attractions between crowders and protein. Here we show that proteins can be destabilized even by crowders that are purely repulsive. With a coarse-grained sequence-based model, we study the folding thermodynamics of two sequences with different native folds, a helical hairpin and a β-barrel, in a range of crowder volume fractions, φc. We find that the native state, N, remains structurally unchanged under crowded conditions, while the size of the unfolded state, U, decreases monotonically with φc. Hence, for all φc>0, U is entropically disfavored relative to N. This entropy-centric view holds for the helical hairpin protein, which is stabilized under all crowded conditions as quantified by changes in either the folding midpoint temperature, Tm, or the free energy of folding. We find, however, that the β-barrel protein is destabilized under low-T, low-φc conditions. This destabilization can be understood from two characteristics of its folding: 1) a relatively compact U at T<Tm, such that U is only weakly disfavored entropically by the crowders; and 2) a transient, compact, and relatively low-energy nonnative state that has a maximum population of only a few percent at φc=0, but increasing monotonically with φc. Overall, protein destabilization driven by hard-core effects appears possible when a compaction of U leads to even a modest population of compact nonnative states that are energetically competitive with N.
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Affiliation(s)
- Saman Bazmi
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St Johns, Newfoundland and Labrador, Canada
| | - Stefan Wallin
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St Johns, Newfoundland and Labrador, Canada.
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8
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Wang S, Wang M, Han L, Sun Y, Cai W, Shao X. Insight into the stability of protein in confined environment through analyzing the structure of water by temperature-dependent near-infrared spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120581. [PMID: 34776375 DOI: 10.1016/j.saa.2021.120581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/13/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
To understand the stability of protein in confined environment, the near-infrared (NIR) spectra of aqueous solutions and reverse micelles (RMs) containing bovine serum albumin (BSA), human serum albumin (HSA) and ovalbumin (OVA) were measured at different temperature. With the resolution enhanced spectra calculated by continuous wavelet transform (CWT), the intensity change of the α-helix band at 4617 cm-1 with temperature shows a clear denaturation of the protein in aqueous solution but not in RMs. The effect of the confined environment on the stability of the proteins is indicated. More importantly, the intensity change of the spectral bands of water around 6956 and 6842 cm-1 provide an evidence for the denaturation, suggesting that water can be a probe exhibiting the structural change of proteins. Furthermore, comparing the spectral features of different water structures obtained by principal component analysis (PCA) from the spectra of RM with and without BSA, it is demonstrated that the bridging water connecting NH in protein and SO in the inner surface of RM may be the reason for the stabilization.
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Affiliation(s)
- Shiying Wang
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, PR China
| | - Mian Wang
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, PR China
| | - Li Han
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, PR China
| | - Yan Sun
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, PR China
| | - Wensheng Cai
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, PR China
| | - Xueguang Shao
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, PR China.
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9
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Ghosh S, Saurabh A, Prabhu NP. Spectroscopic studies on the stability and nucleation-independent fibrillation of partially-unfolded proteins in crowded environment. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 264:120307. [PMID: 34461523 DOI: 10.1016/j.saa.2021.120307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/30/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
Fibril formation of globular proteins is driven by attaining an appropriate partially-unfolded conformation. Excluded volume effect exerted by the presence of other macromolecules in the solution, as found in the cellular interior, might affect the conformational state of proteins and alter their fibril formation process. The change in structure, stability and rate of fibril formation of aggregation-prone partially-unfolded states of lysozyme (Lyz) and α-lactalbumin (ALA) in the presence of different sizes of polyethylene glycol (PEG) is examined using spectroscopic methods. Thermal denaturation and far-UV CD studies suggest that Lyz is stabilized by PEGs and the stability increases with increasing concentration of PEGs. However, the stability of ALA depends on the size and concentration of PEG. The change in enthalpy of unfolding indicates the existence of soft-interactions between the proteins and PEG along with excluded volume effect. Fibrillation rate of Lyz is not significantly altered in the presence of lower concentrations of PEGs suggesting that the crowding effect dominates the viscosity-induced retardation of protein association whereas at higher concentrations the rates are reduced. In case of ALA, the rate of fibrillation is drastically reduced; however, there is a marginal increase with the increasing concentration of PEG. The results suggest that the fibril formation is influenced by change in initial conformation of the partially-unfolded states of the proteins and their stability in the presence of the crowding agent. Further, the size and concentration of the crowding agent, and the soft-interaction between the proteins and PEG also affects the fibrillation.
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Affiliation(s)
- Subhasree Ghosh
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - Archi Saurabh
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - N Prakash Prabhu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India.
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Sung HL, Nesbitt DJ. Effects of Molecular Crowders on Single-Molecule Nucleic Acid Folding: Temperature-Dependent Studies Reveal True Crowding vs Enthalpic Interactions. J Phys Chem B 2021; 125:13147-13157. [PMID: 34813337 DOI: 10.1021/acs.jpcb.1c07852] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Biomolecular folding in cells can be strongly influenced by spatial overlap/excluded volume interactions (i.e., "crowding") with intracellular solutes. As a result, traditional in vitro experiments with dilute buffers may not accurately recapitulate biomolecule folding behavior in vivo. In order to account for such ubiquitous excluded volume effects, biologically inert polyethylene glycol (PEG) and polysaccharides (dextran and Ficoll) are often used as in vitro crowding agents to mimic in vivo crowding conditions, with a common observation that high concentrations of these polymers stabilize the more compact biomolecule conformation. However, such an analysis can be distorted by differences in polymer interactions with the folded vs unfolded conformers, requiring temperature-dependent analysis of the thermodynamics to reliably assess competing enthalpic vs entropic contributions and thus the explicit role of excluded volume. In this work, temperature-controlled single-molecule fluorescence resonance energy transfer (smFRET) is used to characterize the thermodynamic interaction between nucleic acids and common polymer crowders PEG, dextran, and Ficoll. The results reveal that PEG promotes secondary and tertiary nucleic acid folding by simultaneously increasing the folding rate while decreasing the unfolding rate, with temperature-dependent studies confirming that the source of PEG stabilization is predominantly entropic and consistent with a true excluded volume crowding mechanism. By way of contrast, neither dextran nor Ficoll induces any significant concentration-dependent change in nucleic acid folding stability at room temperature, but instead, stabilization effects gradually appear with a temperature increase. Such a thermal response indicates that both folding enthalpies and entropies are impacted by dextran and Ficoll. A detailed thermodynamic analysis of the kinetics suggests that, instead of true entropic molecular crowding, dextran and Ficoll associate preferentially with the unfolded vs folded nucleic acid conformer as a result of larger solvent accessible surface area, thereby skewing the free energy landscapes through both significant entropic/enthalpic contributions that compete and fortuitously cancel near room temperature.
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Affiliation(s)
- Hsuan-Lei Sung
- JILA, National Institute of Standards and Technology, University of Colorado, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - David J Nesbitt
- JILA, National Institute of Standards and Technology, University of Colorado, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States.,Department of Physics, University of Colorado, Boulder, Colorado 80309, United States
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Parray ZA, Naqvi AAT, Ahmad F, Hassan MI, Islam A. Characterization of different intermediate states in myoglobin induced by polyethylene glycol: A process of spontaneous molecular self-organization foresees the energy landscape theory via in vitro and in silico approaches. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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12
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Muñoz-Santiburcio D, Marx D. Confinement-Controlled Aqueous Chemistry within Nanometric Slit Pores. Chem Rev 2021; 121:6293-6320. [PMID: 34006106 DOI: 10.1021/acs.chemrev.0c01292] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this Focus Review, we put the spotlight on very recent insights into the fascinating world of wet chemistry in the realm offered by nanoconfinement of water in mechanically rather rigid and chemically inert planar slit pores wherein only monolayer and bilayer water lamellae can be hosted. We review the effect of confinement on different aspects such as hydrogen bonding, ion diffusion, and charge defect migration of H+(aq) and OH-(aq) in nanoconfined water depending on slit pore width. A particular focus is put on the strongly modulated local dielectric properties as quantified in terms of anisotropic polarization fluctuations across such extremely confined water films and their putative effects on chemical reactions therein. The stunning findings disclosed only recently extend wet chemistry in particular and solvation science in general toward extreme molecular confinement conditions.
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Affiliation(s)
- Daniel Muñoz-Santiburcio
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.,CIC nanoGUNE BRTA, Tolosa Hiribidea 76, 20018 San Sebastián, Spain
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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Structural Refolding and Thermal Stability of Myoglobin in the Presence of Mixture of Crowders: Importance of Various Interactions for Protein Stabilization in Crowded Conditions. Molecules 2021; 26:molecules26092807. [PMID: 34068693 PMCID: PMC8126177 DOI: 10.3390/molecules26092807] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 11/16/2022] Open
Abstract
The intracellular environment is overcrowded with a range of molecules (small and large), all of which influence protein conformation. As a result, understanding how proteins fold and stay functional in such crowded conditions is essential. Several in vitro experiments have looked into the effects of macromolecular crowding on different proteins. However, there are hardly any reports regarding small molecular crowders used alone and in mixtures to observe their effects on the structure and stability of the proteins, which mimics of the cellular conditions. Here we investigate the effect of different mixtures of crowders, ethylene glycol (EG) and its polymer polyethylene glycol (PEG 400 Da) on the structural and thermal stability of myoglobin (Mb). Our results show that monomer (EG) has no significant effect on the structure of Mb, while the polymer disrupts its structure and decreases its stability. Conversely, the additive effect of crowders showed structural refolding of the protein to some extent. Moreover, the calorimetric binding studies of the protein showed very weak interactions with the mixture of crowders. Usually, we can assume that soft interactions induce structural perturbations while exclusion volume effects stabilize the protein structure; therefore, we hypothesize that under in vivo crowded conditions, both phenomena occur and maintain the stability and function of proteins.
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14
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Nasreen K, Parray ZA, Shamsi A, Ahmad F, Ahmed A, Malik A, Lakhrm NA, Hassan MI, Islam A. Crowding Milleu stabilizes apo-myoglobin against chemical-induced denaturation: Dominance of hardcore repulsions in the heme devoid protein. Int J Biol Macromol 2021; 181:552-560. [PMID: 33744250 DOI: 10.1016/j.ijbiomac.2021.03.089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 12/27/2022]
Abstract
Macromolecular crowding can have significant consequences on the structure and dynamics of a protein. The size and shape of a co-solute molecule and the nature of protein contribute significantly in macromolecular crowding, which results in different outcomes in similar conditions. The structure of apo-myoglobin (apo-Mb) both in the absence and presence of denaturants (GdmCl and urea) was investigated in crowded conditions at pH 7.0, with a comparable size of crowders (~70 kDa) but of different shapes (ficoll and dextran) at various concentrations using spectroscopic techniques like absorption and circular dichroism to monitor changes in secondary and tertiary structure, respectively. The crowders in the absence of denaturants showed structural stabilization of the tertiary structure while no significant change in the secondary structure was observed. The effect of crowders on the stability of the protein was also investigated using probes such as Δε291 and θ222 using chemical denaturants. The analysis of chemical-induced denaturation curves showed that both the crowders stabilize apo-Mb by increasing the values of the midpoint of transition (Cm) and change in free energy in the absence of denaturant (∆GD°), and it was observed that dextran 70 shows more stabilization than ficoll 70 under similar conditions. In this study apo-Mb showed stabilization under crowded conditions, which is a deviation from earlier work from our group where holo form of the same protein was destabilized. This study emphasizes that volume exclusion is a dominant force in a simple protein while soft interactions may play important role in the proteins that are possessing prosthetic group. Hence, the effect of crowders is protein-dependent, and excluded volume plays a great role in the stabilization of apo-Mb, which does not interact with the crowders.
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Affiliation(s)
- Khalida Nasreen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Zahoor Ahmad Parray
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Anas Shamsi
- 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
| | - Anwar Ahmed
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ajamaluddin Malik
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Nasser Abobakr Lakhrm
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - 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.
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Parray ZA, Ahmad F, Hassan MI, Islam A. Conformational changes in cytochrome c directed by ethylene glycol accompanying complex formation: Protein-solvent preferential interaction or/and kosmotropic effect. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 242:118788. [PMID: 32810818 DOI: 10.1016/j.saa.2020.118788] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/04/2020] [Accepted: 07/19/2020] [Indexed: 06/11/2023]
Abstract
When proteins interact with solvent or co-solutes with a high specificity and affinity, protein-ligand complexes may be formed. Such phenomenon may involve the processes like intra- and intermolecular interactions, which result in interaction based protein folding. In this study, cytochrome c (cyt c) was treated with different concentrations of ethylene glycol (EG) in crowded and confined media to check its structural stability using various spectroscopic techniques at pH 7.0 and 25 °C. The various spectroscopic techniques including circular dichroism (Soret, far- and near-UV regions), Fourier transform infrared (FTIR), absorption (UV and visible) and Trp fluorescence shows both secondary and tertiary structure of cyt c increases when treated with EG. The investigations using dynamic light scattering (DLS), time resolved fluorescence and isothermal titration calorimetry (ITC) for binding studies shows weak interaction between EG and cyt c. Small increase in the structure of the protein and insignificant decrease in hydrodynamic radii of the protein was observed from the studies. Molecular docking studies showed that EG has binding site on the protein and interact with few amino acid residues by weak interactions such as van der Waals and hydrogen bonding. This study helps in understanding the protein-ligand interactions, provides facts and the mechanisms that mediates the recognition of binding site for specific ligand to the receptor protein, which make possible of the discovery, design, and development of drugs at molecular level without affecting proteins within an organism.
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Affiliation(s)
- Zahoor Ahmad Parray
- 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
| | - 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.
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16
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Hasan S, Isar M, Naeem A. Macromolecular crowding stabilises native structure of α-chymotrypsinogen-A against hexafluoropropanol-induced aggregates. Int J Biol Macromol 2020; 164:3780-3788. [PMID: 32835802 DOI: 10.1016/j.ijbiomac.2020.08.149] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 08/06/2020] [Accepted: 08/19/2020] [Indexed: 12/20/2022]
Abstract
Cell interior is extremely congested with tightly packed biological macromolecules that exerts macromolecular crowding effect, influencing biophysical properties of proteins. To have a deeper insight into it we studied consequences of crowding on aggregation susceptibility and structural stability of α-chymotrypsinogen-A, pro-enzyme of serine protease family, upon addition of co-solvent reported to exert stress on polypeptides crafting favourable conditions for aggregation. Hexafluoropropan-2-ol (HFIP), a fluorinated alcohol caused structural disruption at 5% v/v unveiled by reduced intrinsic intensity and blue shifted ANS spectra. Significantly enhanced, red-shifted ThT and Congo red spectra sustained conformational changes concomitant with aggregation. FTIR and CD results confirmed transition of native structure to non-native extended, cross-linked beta-sheets. Transmission electron micrographs visibly exhibited incidence of amorphous aggregates. Macromolecular crowding, typically mimicked by concentrated solutions of dextran 70, was noticeably witnessed to defend conformational stability under denaturing condition. The native structure was retained maximally in presence of 100 mg/ml followed by 200 and 300 mg/ml dextran indicating concentration dependent deceleration of aggregate formation. It can be established that explicit consideration of crowding effects using relevant range of inert crowding agents must be a requisite for presumptions on intracellular conformational behaviour of proteins deduced from in vitro experiments.
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Affiliation(s)
- Samra Hasan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, U.P., India
| | - Mohd Isar
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, U.P., India
| | - Aabgeena Naeem
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, U.P., India.
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17
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Effects of macromolecular crowding on the folding and aggregation of glycosylated MUC5AC. Biochem Biophys Res Commun 2020; 529:984-990. [PMID: 32819609 DOI: 10.1016/j.bbrc.2020.06.156] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 06/29/2020] [Indexed: 12/28/2022]
Abstract
OBJECTIVE To investigate the effects of macromolecular crowding on the folding and aggregation of MUC5AC with different levels of glycosylation during refolding. METHODS Part 1:An in vitro catalytic reaction comprising the ppGalNAc T2 enzyme, uridine-5'-diphospho-N-galactosamine (UDP-GalNAc) and an 11-amino acid peptide substrate, was used to assess the enzyme activity of the ppGalNAc T2 enzyme in macromolecular crowding environment respectively with bovine serum albumin (BSA), polyethylene glycol (PEG2000), Dextran70 and Ficoll70 at different concentration and temperature. Part 2: The recombinant MUC5AC was expressed in HEK293 cells and purified by nickel column chromatography. The purified protein was treated with PNGase F, and the degree of glycosylation was analyzed by SDS-PAGE. Macromolecular crowding was simulated using PEG2000 at the concentrations of 50, 100, and 200 g/L. Deglycosylated-MUC5AC (d-MUC5AC) and glycosylated MUC5AC (g-MUC5AC) were denatured by GdnHCl and renatured by dilution in a refolding buffer. Protein aggregation was monitored continuously by absorbance reading at 488 nm using a UV spectrophotometer at 25 °C. The refolded proteins were centrifuged, the protein concentration of the supernatant was measured, and refolding yield in different refolding buffers was determined. RESULTS Enzyme activityof ppGalNAc T2 was observed to increase with increasing crowding agent concentration, with highest enzyme activity at 200 g/L. Compared with the group in the absence of crowding reagent, the refolding yield of g-MUC5AC and d-MUC5AC were reduced significantly in the presence of different concentrations of PEG2000 (200, 100, and 50 g/L). Compared with the dilute solution, aggregation increased significantly in the presence of PEG2000, especially at 200 g/L. Moreover, in the crowded reagent with the same concentration, the refolding yield of d-MUC5AC was higher than that of g-MUC5AC, whereas the degree of aggregation of d-MUC5AC was lower than that of g-MUC5AC. CONCLUSION The crowded intracellular environment reduces the refolding rate of MUC5AC and strongly induces the misfolding and aggregation of glycosylated MUC5AC.
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Parray Z, Ahmad F, Hassan MI, Hasan I, Islam A. Effects of Ethylene Glycol on the Structure and Stability of Myoglobin Using Spectroscopic, Interaction, and In Silico Approaches: Monomer Is Different from Those of Its Polymers. ACS OMEGA 2020; 5:13840-13850. [PMID: 32566850 PMCID: PMC7301589 DOI: 10.1021/acsomega.0c01185] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 05/25/2020] [Indexed: 06/11/2023]
Abstract
Investigation of changes in thermal stabilities and structures of proteins in the presence of different co-solutes (ligands) is an integral part in the basic research, discovery, and development of drugs. Ethylene glycol (EG) is known to be toxic and causes teratogenic, inducing primarily skeletal and external malformations and other diseases. The effect of EG on the structure and thermal stability of myoglobin (Mb) was studied using various spectroscopic techniques at pH 7.0 and two different temperatures. As revealed by circular dichroism, Trp fluorescence, nano-DSF, and absorption (UV and visible) measurements, EG (i) has no significant effect on secondary and tertiary structures of Mb at 25 °C, and (ii) it decreases the thermal stability of the protein, which increases with increasing concentration of EG. As revealed by ANS (8-anilino-1-naphthalene sulfonic acid) fluorescence measurements, heat-induced denatured protein has newly exposed hydrophobic patches that bind to ANS. Isothermal titration calorimetry revealed that the interaction between EG and Mb is temperature dependent; the preferential interaction of EG is entropy driven at low temperature, 298 K (25 °C), and it is enthalpy driven at higher temperature, 343 K (70 °C). Molecular docking study showed that EG interacts with side chains of amino acid residues of Mb through van der Waals interactions and hydrogen bonding.
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Affiliation(s)
- Zahoor
Ahmad Parray
- 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
| | - Md Imtaiyaz Hassan
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Ikramul Hasan
- Department
of Basic Medical Science, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha 110025, KSA
| | - Asimul Islam
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
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Interactions Under Crowding Milieu: Chemical-Induced Denaturation of Myoglobin is Determined by the Extent of Heme Dissociation on Interaction with Crowders. Biomolecules 2020; 10:biom10030490. [PMID: 32210191 PMCID: PMC7175338 DOI: 10.3390/biom10030490] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/06/2020] [Accepted: 03/08/2020] [Indexed: 12/13/2022] Open
Abstract
Generally, in vivo function and structural changes are studied by probing proteins in a dilute solution under in vitro conditions, which is believed to be mimicking proteins in intracellular milieu. Earlier, thermal-induced denaturation of myoglobin, in the milieu of crowder molecule showed destabilization of the metal protein. Destabilization of protein by thermal-induced denaturation involves a large extrapolation, so, the reliability is questionable. This led us to measure the effects of macromolecular crowding on its stability by chemical-induced denaturation of the protein using probes like circular dichroism and absorption spectroscopy in the presence of dextran 70 and ficoll 70 at various pHs (acidic: 6.0, almost neutral: 7.0 and basic: 8.0). Observations showed that the degree of destabilization of myoglobin was greater due to ficoll 70 as compared to that of dextran 70 so it can be understood that the nature of the crowder or the shape of the crowder has an important role towards the stability of proteins. Additionally, the degree of destabilization was observed as pH dependent, however the pH dependence is different for different crowders. Furthermore, isothermal titration calorimetry and molecular docking studies confirmed that both the crowders (ficoll and dextran) bind to heme moiety of myoglobin and a single binding site was observed for each.
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20
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Abstract
When compressed in a slit of width D, a Θ-chain that displays the scaling of size R0 (diameter) with respect to the number of monomers N, R0 ∼ aN1/2, expands in the lateral direction as R|| ∼ aNν(a/D)2ν-1. Provided that the Θ condition is strictly maintained throughout the compression, the well-known scaling exponent of Θ-chain in two dimensions, ν = 4/7, is anticipated in a perfect confinement. However, numerics shows that upon increasing compression from R0/D < 1 to R0/D ≫ 1, ν gradually deviates from ν = 1/2 and plateaus at ν = 3/4, the exponent associated with the self-avoiding walk in two dimensions. Using both theoretical considerations and numerics, we argue that it is highly nontrivial to maintain the Θ condition under confinement because of two major effects. First, as the dimension is reduced from three to two dimensions, the contributions of higher order virial terms, which can be ignored in three dimensions at large N, become significant, making the perturbative expansion used in Flory-type approach inherently problematic. Second and more importantly, the geometrical confinement, which is regarded as an applied external field, alters the second virial coefficient (B2) changes from B2 = 0 (Θ condition) in free space to B2 > 0 (good-solvent condition) in confinement. Our study provides practical insight into how confinement affects the conformation of a single polymer chain.
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Affiliation(s)
- Lei Liu
- Korea Institute for Advanced Study , Seoul 02455 , Korea
| | - Philip A Pincus
- Physics and Material Department , University of California , Santa Barbara , California 93106 , United States
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21
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22
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Parray ZA, Ahamad S, Ahmad F, Hassan MI, Islam A. First evidence of formation of pre-molten globule state in myoglobin: A macromolecular crowding approach towards protein folding in vivo. Int J Biol Macromol 2018; 126:1288-1294. [PMID: 30586590 DOI: 10.1016/j.ijbiomac.2018.12.170] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/14/2018] [Accepted: 12/18/2018] [Indexed: 01/04/2023]
Abstract
Myoglobin is known to show formation of intermediate states under various environmental conditions, in spite of that, this is the first evidence of formation pre-molten globule (PMG) in myoglobin. Polyethylene glycol (PEG) of various molecular sizes shows assorted effects on different proteins. Out of too short and too long PEGs, only PEGs of optimal size interact with proteins leading to change in protein structure that form intermediate state. We are the first one to report the formation of PMG in a protein in the presence of a crowding agent. The PEG-induced intermediate state was characterized by various techniques like absorption, fluorescence, near- and far-UV circular dichroism spectroscopy, ANS binding, and dynamic light scattering measurements to be PMG. Isothermal titration calorimetry and docking studies were further carried out to delineate the mechanism of formation of PMG in myoglobin in physiological conditions. The intermediate formed due to interaction of PEG with myoglobin has physiological implications which are essential to unravel the mystery to solve the massively complicated problems involved in the proper folding of proteins in vivo. Further, outcomes from this study are expected to gain mechanistic insights on the native structure and functions of proteins under in vivo conditions.
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Affiliation(s)
- Zahoor Ahmad Parray
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Shahzaib Ahamad
- 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
| | - 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.
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23
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Das N, Sen P. Structural, Functional, and Dynamical Responses of a Protein in a Restricted Environment Imposed by Macromolecular Crowding. Biochemistry 2018; 57:6078-6089. [DOI: 10.1021/acs.biochem.8b00599] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Nilimesh Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208 016, India
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208 016, India
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24
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Kumar R, Sharma D, Kumar V, Kumar R. Factors defining the effects of macromolecular crowding on dynamics and thermodynamic stability of heme proteins in-vitro. Arch Biochem Biophys 2018; 654:146-162. [DOI: 10.1016/j.abb.2018.07.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 11/28/2022]
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25
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Siddiqui GA, Naeem A. Aggregation of globular protein as a consequences of macromolecular crowding: A time and concentration dependent study. Int J Biol Macromol 2018; 108:360-366. [DOI: 10.1016/j.ijbiomac.2017.12.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 11/30/2017] [Accepted: 12/01/2017] [Indexed: 12/11/2022]
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26
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Sett R, Sen S, Paul BK, Guchhait N. How Does Nanoconfinement within a Reverse Micelle Influence the Interaction of Phenazinium-Based Photosensitizers with DNA? ACS OMEGA 2018; 3:1374-1385. [PMID: 31458466 PMCID: PMC6641382 DOI: 10.1021/acsomega.7b01820] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/17/2018] [Indexed: 06/10/2023]
Abstract
The major focus of the present work lies in exploring the influence of nanoconfinement within aerosol-OT (AOT) reverse micelles on the binding interaction of two phenazinium-based photosensitizers, namely, phenosafranin (PSF) and safranin-O (SO), with the DNA duplex. Circular dichroism and dynamic light-scattering studies reveal the condensation of DNA within the reverse micellar interior (transformation of the B-form of native DNA to ψ-form). Our results unveil a remarkable effect of the degree of hydration of the reverse micellar core on the stability of the stacking interaction (intercalation) of the drugs (PSF and SO) into DNA; increasing size of the water nanopool (that is, w 0) accompanies decreasing curvature of the DNA duplex structure with the consequent effect of increasing stabilization of the drug:DNA intercalation. The marked differences in the dynamical aspects of the interaction scenario following encapsulation within the reverse micellar core and the subsequent dependence on the size of the water nanopool are also meticulously explored. The differential degrees of steric interactions offered by the drug molecules (presence of methyl substitutions on the planar phenazinium ring in SO) are also found to affect the extent of intercalation of the drugs to DNA. In this context, it is imperative to state that the water pool of the reverse micellar core is often argued to approach bulk-like properties of water with increasing micellar size (typically w 0 ≥ 10), so that deviation from the bulk water properties is likely to be minimized in large reverse micelles (w 0 ≥ 10). On the contrary, our results (particularly quantitative elucidation of micropolarity and dynamical aspects of the interaction) explicitly demonstrate that the bulk-like behavior of the nanoconfined water is not truly achieved even in large reverse micelles.
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Affiliation(s)
- Riya Sett
- Department
of Chemistry, University of Calcutta, 92 A. P. C. Road, Kolkata 700009, India
| | - Swagata Sen
- Department
of Chemistry, University of Calcutta, 92 A. P. C. Road, Kolkata 700009, India
| | - Bijan K. Paul
- Department
of Chemistry, Mahadevananda Mahavidyalaya, Barrackpore, Kolkata 700120, India
| | - Nikhil Guchhait
- Department
of Chemistry, University of Calcutta, 92 A. P. C. Road, Kolkata 700009, India
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27
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Gehlot P, Kulshrestha A, Bharmoria P, Damarla K, Chokshi K, Kumar A. Surface-Active Ionic Liquid Cholinium Dodecylbenzenesulfonate: Self-Assembling Behavior and Interaction with Cellulase. ACS OMEGA 2017; 2:7451-7460. [PMID: 31457311 PMCID: PMC6644741 DOI: 10.1021/acsomega.7b01291] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 10/17/2017] [Indexed: 06/10/2023]
Abstract
The conventional sodium dodecylbenzenesulfonate (NaDBS) has been converted into an efficient and nontoxic anionic surface-active ionic liquid, cholinium dodecylbenzenesulfonate (Cho[DBS]). We have investigated its self-assembling behavior, interaction with the enzyme cellulase, and ecotoxicity. The surface-active properties at the air-liquid interface and the aggregation behavior of Cho[DBS] in water have been determined using tensiometry, isothermal titration calorimetry (ITC), conductometry, and dynamic light scattering (DLS). The enzyme activity was observed using dinitro salicylic acid analysis. The enhanced enzyme activity was explained through active-site exfoliation and structural constancy of cellulase in the micellar medium using the results from fluorescence, circular dichroism, DLS, and ITC. The nontoxic nature was confirmed by toxicity analysis on the freshwater microalgae Scenedesmus sp.
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Affiliation(s)
- Praveen
Singh Gehlot
- Academy
of Scientific and Innovative Research (AcSIR), Salt and Marine
Chemicals Discipline, and Salt and Marine Chemicals Discipline, Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar 364002, Gujarat, India
| | - Akshay Kulshrestha
- Academy
of Scientific and Innovative Research (AcSIR), Salt and Marine
Chemicals Discipline, and Salt and Marine Chemicals Discipline, Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar 364002, Gujarat, India
| | - Pankaj Bharmoria
- Academy
of Scientific and Innovative Research (AcSIR), Salt and Marine
Chemicals Discipline, and Salt and Marine Chemicals Discipline, Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar 364002, Gujarat, India
| | - Krishnaiah Damarla
- Academy
of Scientific and Innovative Research (AcSIR), Salt and Marine
Chemicals Discipline, and Salt and Marine Chemicals Discipline, Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar 364002, Gujarat, India
| | - Kaumeel Chokshi
- Academy
of Scientific and Innovative Research (AcSIR), Salt and Marine
Chemicals Discipline, and Salt and Marine Chemicals Discipline, Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar 364002, Gujarat, India
| | - Arvind Kumar
- Academy
of Scientific and Innovative Research (AcSIR), Salt and Marine
Chemicals Discipline, and Salt and Marine Chemicals Discipline, Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar 364002, Gujarat, India
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Prototropism and dynamics of an anticancer drug in reverse micelles: Focus on the variation of pH in reverse micelles having w0≥ 10. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.08.076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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29
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Nasreen K, Ahamad S, Ahmad F, Hassan MI, Islam A. Macromolecular crowding induces molten globule state in the native myoglobin at physiological pH. Int J Biol Macromol 2017; 106:130-139. [PMID: 28811208 DOI: 10.1016/j.ijbiomac.2017.08.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 07/26/2017] [Accepted: 08/01/2017] [Indexed: 01/07/2023]
Abstract
Here, we report the formation of molten globule state of the native myoglobin in crowded environment. We have used Soret absorption spectroscopy and far-UV circular dichroism to monitor changes in tertiary and secondary structures of myoglobin, respectively. Our results reveal that in the presence of ficoll 70, the secondary structure of myoglobin remains unchanged while tertiary structure is lost significantly. 1-anilinonaphthalene-8-sulfonate binding experiments showed that myoglobin in the presence of various concentrations of ficoll 70, has newly exposed hydrophobic surfaces. Dynamic light scattering measurements show that there is almost 1.5 times increase in the hydrodynamic volume of myoglobin in the crowded environment. These structural characteristics of myoglobin in the presence of 300mg/ml ficoll 70 resemble those of molten globule state. Isothermal titration calorimetric (ITC) measurements show that ficoll 70 binds to myoglobin, whereas it shows no interaction with apo form of the protein. ITC results indicate that the reason behind this unique behavior of ficoll 70 towards myoglobin may be interaction of ficoll 70 with the heme group of myoglobin, which was further confirmed by the docking studies. We hypothesize that the soft interactions between heme and ficoll 70 leads to the formation of molten globule in myoglobin.
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Affiliation(s)
- Khalida Nasreen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Shahzaib Ahamad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India.
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Kisley L, Miller KA, Guin D, Kong X, Gruebele M, Leckband DE. Direct Imaging of Protein Stability and Folding Kinetics in Hydrogels. ACS APPLIED MATERIALS & INTERFACES 2017; 9:21606-21617. [PMID: 28553706 DOI: 10.1021/acsami.7b01371] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We apply fast relaxation imaging (FReI) as a novel technique for investigating the folding stability and dynamics of proteins within polyacrylamide hydrogels, which have diverse and widespread uses in biotechnology. FReI detects protein unfolding in situ by imaging changes in fluorescence resonance energy transfer (FRET) after temperature jump perturbations. Unlike bulk measurements, diffraction-limited epifluorescence imaging combined with fast temperature perturbations reveals the impact of local environment effects on protein-biomaterial compatibility. Our experiments investigated a crowding sensor protein (CrH2) and phosphoglycerate kinase (PGK), which undergoes cooperative unfolding. The crowding sensor quantifies the confinement effect of the cross-linked hydrogel: the 4% polyacrylamide hydrogel is similar to aqueous solution (no confinement), while the 10% hydrogel is strongly confining. FRAP measurements and protein concentration gradients in the 4% and 10% hydrogels further support this observation. PGK reveals that noncovalent interactions of the protein with the polymer surface are more important than confinement for determining protein properties in the gel: the mere presence of hydrogel increases protein stability, speeds up folding relaxation, and promotes irreversible binding to the polymer even at the solution-gel interface, whereas the difference between the 4% and the 10% hydrogels is negligible despite their large difference in confinement. The imaging capabilities of FReI, demonstrated to be diffraction limited, further revealed spatially homogeneous protein unfolding across the hydrogels at 500 nm length scales and revealed differences in protein properties at the gel-solution boundary.
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Affiliation(s)
- Lydia Kisley
- Beckman Institute for Advanced Science and Technology, ‡Department of Chemistry, §Department of Biochemistry, ∥Department of Chemical and Biomolecular Engineering, and ⊥Department of Physics, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Kali A Miller
- Beckman Institute for Advanced Science and Technology, ‡Department of Chemistry, §Department of Biochemistry, ∥Department of Chemical and Biomolecular Engineering, and ⊥Department of Physics, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Drishti Guin
- Beckman Institute for Advanced Science and Technology, ‡Department of Chemistry, §Department of Biochemistry, ∥Department of Chemical and Biomolecular Engineering, and ⊥Department of Physics, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Xinyu Kong
- Beckman Institute for Advanced Science and Technology, ‡Department of Chemistry, §Department of Biochemistry, ∥Department of Chemical and Biomolecular Engineering, and ⊥Department of Physics, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Martin Gruebele
- Beckman Institute for Advanced Science and Technology, ‡Department of Chemistry, §Department of Biochemistry, ∥Department of Chemical and Biomolecular Engineering, and ⊥Department of Physics, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Deborah E Leckband
- Beckman Institute for Advanced Science and Technology, ‡Department of Chemistry, §Department of Biochemistry, ∥Department of Chemical and Biomolecular Engineering, and ⊥Department of Physics, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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Jia J, Peng X, Qi W, Su R, He Z. Effects of macromolecular crowding on alkaline phosphatase unfolding, conformation and stability. Int J Biol Macromol 2017; 101:373-382. [PMID: 28344089 DOI: 10.1016/j.ijbiomac.2017.03.113] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 02/27/2017] [Accepted: 03/21/2017] [Indexed: 10/19/2022]
Abstract
The interior of the cell is tightly packed with various biological macromolecules, which affects physiological processes, especially protein folding process. To explore how macromolecular crowding may influence protein folding process, alkaline phosphatase (ALP) was chosen as a model protein, and the unfolding process of ALP induced by GdnHCl was studied in the presence of crowding agents such as PEG 4000, Dextran 70 and Ficoll 70. The effect of macromolecular crowding on the denatured state of ALP was directly probed by measuring enzyme activities, fluorescence spectroscopy and circular dichroism. From the results of circular dichroism, GdnHCl induced a biphasic change, suggesting that a three-state unfolding mechanism was involved in the denaturation process irrespective of the absence or presence of crowding agents. It was also found that crowding agents had a little impact on the unfolding process of ALP. The results of phase diagrams also demonstrated that the unfolding process of ALP induced by GdnHCl was three-state mechanism. Moreover, the results of fluorescence spectra demonstrated that with the increase of GdnHCl concentration, the structure of protein had changed, but existence of crowding agents can make protein structure more stable. Our results can provide valuable information for understanding the protein folding in vivo.
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Affiliation(s)
- Jiajia Jia
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Xin Peng
- School of Life Sciences, Tianjin University, Tianjin 300072, PR China.
| | - Wei Qi
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China; State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, PR China; Collaborative Innovation Center of Chemistry Science and Engineering (Tianjin), Tianjin 300072, PR China; Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin, 300072, PR China.
| | - Rongxin Su
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China; State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, PR China; Collaborative Innovation Center of Chemistry Science and Engineering (Tianjin), Tianjin 300072, PR China; Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin, 300072, PR China
| | - Zhimin He
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China; State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, PR China
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32
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Kaur A, Banipal PK, Banipal TS. Study on the interactional behaviour of transition metal ions with myoglobin: A detailed calorimetric, spectroscopic and light scattering analysis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 174:236-244. [PMID: 27923210 DOI: 10.1016/j.saa.2016.11.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/14/2016] [Accepted: 11/24/2016] [Indexed: 06/06/2023]
Abstract
The energetics and the impact on the conformation of heme containing protein myoglobin (Mb) due to the binding of three transition metal ions (Zn2+, Ni2+, and Mn2+) have been investigated using isothermal titration calorimetry (ITC), dynamic light scattering (DLS), UV-vis, and circular dichroism (CD) spectroscopy under physiological conditions. The binding affinity of the order of 104M-1 has been observed for all metal ions from calorimetry as well as from absorption spectroscopy. The binding of these metal ions with Mb is a spontaneous process that exposes the hydrophobic groups away from the protein core as exhibited by the negative Gibbs free energy change (ΔG) and positive heat capacity change (ΔCp) values. Both light scattering and CD results demonstrates that the binding of Zn2+ and Mn2+ ions with Mb results in the folding whereas Ni2+ ion results in the unfolding of the protein. No direct interactions among the transition metal ions and heme moiety of Mb has been observed from absorption study. The results of these studies reveals that Mn2+ ion influences the biological functions of Mb to a larger extent in spite of its lowest affinity followed by Zn2+ and Ni2+ ions.
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Affiliation(s)
- Amandeep Kaur
- Department of Chemistry, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Parampaul K Banipal
- Department of Chemistry, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Tarlok S Banipal
- Department of Chemistry, Guru Nanak Dev University, Amritsar 143005, Punjab, India.
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Patra A, Samanta N, Das DK, Mitra RK. Enhanced Catalytic Activity of α-Chymotrypsin in Cationic Surfactant Solutions: The Component Specificity Revisited. J Phys Chem B 2017; 121:1457-1465. [PMID: 28151666 DOI: 10.1021/acs.jpcb.6b10472] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enhanced catalytic activity (super activity) of enzymes in the presence of surfactants is of key importance in "micellar enzymology"; such super activity is not very trivial, it is highly system specific, and the mechanism behind the activity enhancement is not always well apprehended. We report the catalytic activity of α-chymotrypsin (CHT) on ala-ala-phe-7-amido-4-methylcoumarin (AMC) in the presence of cationic surfactants of different hydrophobic chain lengths: dodecyltrimethylammonium bromide (DTAB), cetyltrimethylammonium bromide (CTAB) and octadecyltrimethylammonium bromide (OTAB). It is observed that in comparison to buffer the catalytic activity of CHT is enhanced 5-fold in premicellar DTAB solutions, while negligible changes are observed in CTAB and OTAB. Activity decreases considerably in the post micellar concentration, specifically for the latter two surfactants. A similar trend is also obtained in another substrate 2-napthyal acetate hydrolysis. Such surfactant specific superactivity is intriguing. The protein's secondary and tertiary structures in the presence of these surfactants are determined using circular dichroism (CD) spectroscopy and it is found that both CTAB and OTAB perturb the protein structure significantly, especially in the post micellar concentrations. DTAB, on the other hand, does not produce noticeable changes in the protein structure. The various pairwise interactions present in the system have been underlined using both steady-state and time-resolved fluorescence spectroscopy. Assuming a three-step kinetics model, we determine the free energy changes of the reaction, and the observations have been discussed in the light of the various interactions among the components.
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Affiliation(s)
- Animesh Patra
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences , Block JD, Sector III, Salt Lake, Kolkata 700106, India
| | - Nirnay Samanta
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences , Block JD, Sector III, Salt Lake, Kolkata 700106, India
| | - Dipak Kumar Das
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences , Block JD, Sector III, Salt Lake, Kolkata 700106, India
| | - Rajib Kumar Mitra
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences , Block JD, Sector III, Salt Lake, Kolkata 700106, India
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Fonin AV, Silonov SA, Sitdikova AK, Kuznetsova IM, Uversky VN, Turoverov KK. Structure and Conformational Properties of d-Glucose/d-Galactose-Binding Protein in Crowded Milieu. Molecules 2017; 22:molecules22020244. [PMID: 28178192 PMCID: PMC6155729 DOI: 10.3390/molecules22020244] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/26/2017] [Accepted: 01/29/2017] [Indexed: 11/18/2022] Open
Abstract
Conformational changes of d-glucose/d-galactose-binding protein (GGBP) were studied under molecular crowding conditions modeled by concentrated solutions of polyethylene glycols (PEG-12000, PEG-4000, and PEG-600), Ficoll-70, and Dextran-70, addition of which induced noticeable structural changes in the GGBP molecule. All PEGs promoted compaction of GGBP and lead to the increase in ordering of its structure. Concentrated solutions of PEG-12000 and PEG-4000 caused GGBP aggregation. Although Ficoll-70 and Dextran-70 also promoted increase in the GGBP ordering, the structural outputs were different for different crowders. For example, in comparison with the GGBP in buffer, the intrinsic fluorescence spectrum of this protein was shifted to short-wave region in the presence of PEGs but was red-shifted in the presence of Ficoll-70 and Dextran-70. It was hypothesized that this difference could be due to the specific interaction of GGBP with the sugar-based polymers (Ficoll-70 and Dextran-70), indicating that protein can adopt different conformations in solutions containing molecular crowders of different chemical nature. It was also shown that all tested crowding agents were able to stabilize GGBP structure shifting the GGBP guanidine hydrochloride (GdnHCl)-induced unfolding curves to higher denaturant concentrations, but their stabilization capabilities did not depend on the hydrodynamic dimensions of the polymers molecules. Refolding of GGBP was complicated by protein aggregation in all tested solutions of crowding agents. The lowest yield of refolded protein was achieved in the highly concentrated solutions of PEG-12000. These data support the previous notion that the influence of macromolecular crowders on proteins is rather complex phenomenon that extends beyond the excluded volume effects.
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Affiliation(s)
- Alexander V Fonin
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Structural Dynamics, Stability and Folding of Proteins, Tikhoretsky av. 4, St. Petersburg 197046, Russia.
| | - Sergey A Silonov
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Structural Dynamics, Stability and Folding of Proteins, Tikhoretsky av. 4, St. Petersburg 197046, Russia.
- Saint-Petersburg Technological Institute (Technical University), Moskovsky av. 26, Saint-Petersburg 190013, Russia.
| | - Asiya K Sitdikova
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Structural Dynamics, Stability and Folding of Proteins, Tikhoretsky av. 4, St. Petersburg 197046, Russia.
- Department of Biophysics, St. Petersburg State Polytechnical University, Polytechnicheskaya av. 29, St. Petersburg 195251, Russia.
| | - Irina M Kuznetsova
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Structural Dynamics, Stability and Folding of Proteins, Tikhoretsky av. 4, St. Petersburg 197046, Russia.
| | - Vladimir N Uversky
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Structural Dynamics, Stability and Folding of Proteins, Tikhoretsky av. 4, St. Petersburg 197046, Russia.
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Konstantin K Turoverov
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Structural Dynamics, Stability and Folding of Proteins, Tikhoretsky av. 4, St. Petersburg 197046, Russia.
- Department of Biophysics, St. Petersburg State Polytechnical University, Polytechnicheskaya av. 29, St. Petersburg 195251, Russia.
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Shahid S, Hassan MI, Islam A, Ahmad F. Size-dependent studies of macromolecular crowding on the thermodynamic stability, structure and functional activity of proteins: in vitro and in silico approaches. Biochim Biophys Acta Gen Subj 2017; 1861:178-197. [DOI: 10.1016/j.bbagen.2016.11.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 11/09/2016] [Accepted: 11/10/2016] [Indexed: 11/27/2022]
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36
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Xu G, Cheng K, Wu Q, Liu M, Li C. Confinement Alters the Structure and Function of Calmodulin. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609639] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Guohua Xu
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
| | - Kai Cheng
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
- Graduate University of Chinese Academy of Sciences; Beijing 100029 P.R. China
| | - Qiong Wu
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
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37
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Xu G, Cheng K, Wu Q, Liu M, Li C. Confinement Alters the Structure and Function of Calmodulin. Angew Chem Int Ed Engl 2016; 56:530-534. [DOI: 10.1002/anie.201609639] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 11/11/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Guohua Xu
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
| | - Kai Cheng
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
- Graduate University of Chinese Academy of Sciences; Beijing 100029 P.R. China
| | - Qiong Wu
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P.R. China
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38
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Babayekhorasani F, Dunstan DE, Krishnamoorti R, Conrad JC. Nanoparticle diffusion in crowded and confined media. SOFT MATTER 2016; 12:8407-8416. [PMID: 27714348 DOI: 10.1039/c6sm01543c] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We identify distinct mechanisms controlling slowing of nanoparticle diffusion through complex media featuring both rigid geometrical confinement and soft mobile crowders. Towards this end, we use confocal microscopy and single particle tracking to probe the diffusion of 400 nm nanoparticles suspended in Newtonian water, in a Newtonian glycerol/water mixture, or in a non-Newtonian polymer solution through a model porous medium, a packed bed of microscale glass beads. The mobility of nanoparticles, as quantified by the long-time diffusion coefficient extracted from the particle mean-squared displacement, slows as the average pore size of the packed bed media decreases for both Newtonian and non-Newtonian solutions. The distribution of particle displacements is non-Gaussian, consistent with the spatial heterogeneity of the geometrical confinement imposed by the packed bed. The slowing of nanoparticle mobility in all solutions follows the predictions of models that describe hydrodynamic interactions with the packed bed. In non-Newtonian solutions, depletion interactions due to the polymers near the glass beads result in temporary adsorption of particles onto the bead surface, as indicated by a stretched-exponential distribution of residence times. Our results therefore suggest that the confined diffusive dynamics of nanoparticles in polymer solutions is controlled by two competing mechanisms: hydrodynamic interactions between particles and spatial obstacles, which dictate the long-time slowing of diffusion, and depletion interactions between particles and confining walls due to the macromolecules, which control transient adsorption and hence alter the statistics of the short-time motion.
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Affiliation(s)
| | - Dave E Dunstan
- Chemical and Biomolecular Engineering, University of Melbourne, 3010, Australia
| | - Ramanan Krishnamoorti
- Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, USA. and Department of Chemistry, University of Houston, Houston, Texas 77204, USA
| | - Jacinta C Conrad
- Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, USA.
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39
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Wu Y, Teng N, Li S. Effects of macromolecular crowding and osmolyte on human Tau fibrillation. Int J Biol Macromol 2016; 90:27-36. [DOI: 10.1016/j.ijbiomac.2015.11.091] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 11/13/2015] [Accepted: 11/29/2015] [Indexed: 10/22/2022]
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40
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Kadumuri RV, Gullipalli J, Subramanian S, Jaipuria G, Atreya HS, Vadrevu R. Crowding interactions perturb structure and stability by destabilizing the stable core of the α-subunit of tryptophan synthase. FEBS Lett 2016; 590:2096-105. [PMID: 27311646 DOI: 10.1002/1873-3468.12259] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/06/2016] [Accepted: 06/13/2016] [Indexed: 11/12/2022]
Abstract
The consequences of crowding derived from relatively small and intrinsically disordered proteins are not clear yet. We report the effect of ficoll-70 on the structure and stability of native and partially folded states of the 29 kDa alpha subunit of tryptophan synthase (αTS). Overall, combining the changes in the circular dichroism and fluorescence spectra, in conjunction with the gradual loss of cooperativity under urea denaturation in the presence of increasing amounts of ficoll, it may be concluded that the crowding agent perturbs not only the native state but also the partially folded state of αTS. Importantly, NMR data indicate that ficoll interacts with the residues that constitute the stable core of the protein thus shedding light on the origin of the observed perturbation.
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Affiliation(s)
- Rajashekar Varma Kadumuri
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, India
| | - Jagadeesh Gullipalli
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, India
| | - SriVidya Subramanian
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, India
| | - Garima Jaipuria
- NMR Research Centre, Indian Institute of Science, Bangalore, India
| | | | - Ramakrishna Vadrevu
- Department of Biological Sciences, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Hyderabad, India
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41
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Abstract
![]()
Calcineurin
is a Ser/Thr phosphatase that is important for key
biological processes, including immune system activation. We previously
identified a region in the intrinsically disordered regulatory domain
of calcineurin that forms a critical amphipathic α-helix (the
“distal helix”) that is required for complete activation
of calcineurin. This distal helix was shown to have a Tm close to that of human body temperature. Because the Tm was determined in dilute buffer, we hypothesized
that other factors inherent to a cellular environment might modulate
the stability of the distal helix. One such factor that contributes
to stability in other proteins is macromolecular crowding. The cell
cytoplasm is comprised of up to 400 g/L protein, lipids, nucleic acids,
and other compounds. We hypothesize that the presence of such crowders
could increase the thermal stability of the distal helix and thus
lead to a more robust activation of calcineurin in vivo. Using biophysical and biochemical approaches, we show that the
distal helix of calcineurin is indeed stabilized when crowded by the
synthetic polymers dextran 70 and ficoll 70, and that this stabilization
of the distal helix increases the activity of calcineurin.
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Affiliation(s)
- Erik C Cook
- Center for Structural Biology, Department of Molecular and Cellular Biochemistry, University of Kentucky , 741 South Limestone Street, Lexington, Kentucky 40536-0509, United States
| | - Trevor P Creamer
- Center for Structural Biology, Department of Molecular and Cellular Biochemistry, University of Kentucky , 741 South Limestone Street, Lexington, Kentucky 40536-0509, United States
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42
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Paul SS, Sil P, Chakraborty R, Haldar S, Chattopadhyay K. Molecular Crowding Affects the Conformational Fluctuations, Peroxidase Activity, and Folding Landscape of Yeast Cytochrome c. Biochemistry 2016; 55:2332-43. [DOI: 10.1021/acs.biochem.6b00053] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Simanta Sarani Paul
- Protein
Folding and Dynamics Laboratory, Structural Biology and Bioinformatics
Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C.
Mullick Road, Kolkata 700032, India
| | - Pallabi Sil
- Protein
Folding and Dynamics Laboratory, Structural Biology and Bioinformatics
Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C.
Mullick Road, Kolkata 700032, India
| | - Ritobrita Chakraborty
- Protein
Folding and Dynamics Laboratory, Structural Biology and Bioinformatics
Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C.
Mullick Road, Kolkata 700032, India
| | - Shubhasis Haldar
- Department
of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz
18, 82152 Martinsried, Germany
| | - Krishnananda Chattopadhyay
- Protein
Folding and Dynamics Laboratory, Structural Biology and Bioinformatics
Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C.
Mullick Road, Kolkata 700032, India
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43
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Stepanenko OV, Povarova OI, Sulatskaya AI, Ferreira LA, Zaslavsky BY, Kuznetsova IM, Turoverov KK, Uversky VN. Protein unfolding in crowded milieu: what crowding can do to a protein undergoing unfolding? J Biomol Struct Dyn 2016; 34:2155-70. [PMID: 26474212 DOI: 10.1080/07391102.2015.1109554] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The natural environment of a protein inside a cell is characterized by the almost complete lack of unoccupied space, limited amount of free water, and the tightly packed crowd of various biological macromolecules, such as proteins, nucleic acids, polysaccharides, and complexes thereof. This extremely crowded natural milieu is poorly mimicked by slightly salted aqueous solutions containing low concentrations of a protein of interest. The accepted practice is to model crowded environments by adding high concentrations of various polymers that serve as model "crowding agents" to the solution of a protein of interest. Although studies performed under these model conditions revealed that macromolecular crowding might have noticeable influence on various aspects related to the protein structure, function, folding, conformational stability, and aggregation propensity, the complete picture describing conformational behavior of a protein under these conditions is missing as of yet. Furthermore, there is an accepted belief that the conformational stability of globular proteins increases in the presence crowding agents due to the excluded volume effects. The goal of this study was to conduct a systematic analysis of the effect of high concentrations of PEG-8000 and Dextran-70 on the unfolding behavior of eleven globular proteins belonging to different structural classes.
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Affiliation(s)
- Olga V Stepanenko
- a Laboratory of Structural Dynamics, Stability and Folding of Proteins , Institute of Cytology, Russian Academy of Sciences , St. Petersburg , Russia
| | - Olga I Povarova
- a Laboratory of Structural Dynamics, Stability and Folding of Proteins , Institute of Cytology, Russian Academy of Sciences , St. Petersburg , Russia
| | - Anna I Sulatskaya
- a Laboratory of Structural Dynamics, Stability and Folding of Proteins , Institute of Cytology, Russian Academy of Sciences , St. Petersburg , Russia
| | - Luisa A Ferreira
- b Cleveland Diagnostics , 3615 Superior Ave., Suite 4407B, Cleveland , OH 44114 , USA
| | - Boris Y Zaslavsky
- b Cleveland Diagnostics , 3615 Superior Ave., Suite 4407B, Cleveland , OH 44114 , USA
| | - Irina M Kuznetsova
- a Laboratory of Structural Dynamics, Stability and Folding of Proteins , Institute of Cytology, Russian Academy of Sciences , St. Petersburg , Russia
| | - Konstantin K Turoverov
- a Laboratory of Structural Dynamics, Stability and Folding of Proteins , Institute of Cytology, Russian Academy of Sciences , St. Petersburg , Russia.,c Department of Biophysics , Peter the Great St. Petersburg Polytechnic University , St. Petersburg , 195251 , Russia
| | - Vladimir N Uversky
- a Laboratory of Structural Dynamics, Stability and Folding of Proteins , Institute of Cytology, Russian Academy of Sciences , St. Petersburg , Russia.,d Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine , University of South Florida , Tampa , FL 33612 , USA
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44
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Unusual effects of crowders on heme retention in myoglobin. FEBS Lett 2015; 589:3807-15. [DOI: 10.1016/j.febslet.2015.11.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 11/05/2015] [Accepted: 11/10/2015] [Indexed: 11/24/2022]
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45
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Mittal S, Chowhan RK, Singh LR. Macromolecular crowding: Macromolecules friend or foe. Biochim Biophys Acta Gen Subj 2015; 1850:1822-31. [DOI: 10.1016/j.bbagen.2015.05.002] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/27/2015] [Accepted: 05/04/2015] [Indexed: 12/11/2022]
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46
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Hilaire MR, Abaskharon RM, Gai F. Biomolecular Crowding Arising from Small Molecules, Molecular Constraints, Surface Packing, and Nano-Confinement. J Phys Chem Lett 2015; 6:2546-53. [PMID: 26266732 PMCID: PMC4610718 DOI: 10.1021/acs.jpclett.5b00957] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The effect of macromolecular crowding on the structure, dynamics, and reactivity of biomolecules is well established and the relevant research has been extensively reviewed. Herein, we focus our discussion on crowding effects arising from small cosolvent molecules and densely packed surface conditions. In addition, we highlight recent efforts that capitalize on the excluded volume effect for various tailored biochemical and biophysical applications. Specifically, we discuss how a targeted increase in local mass density can be exploited to gain insight into the folding dynamics of the protein of interest and how confinement via reverse micelles can be used to study a range of biophysical questions, from protein hydration dynamics to amyloid formation.
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Affiliation(s)
| | | | - Feng Gai
- To whom correspondence should be addressed; ; Phone: 215-573-6256; Fax: 215-573-2112
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Biswas S, Chowdhury PK. Unusual domain movement in a multidomain protein in the presence of macromolecular crowders. Phys Chem Chem Phys 2015; 17:19820-33. [DOI: 10.1039/c5cp02674a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
FRET-based distance changes between domains I and II of HSA reveal significant differences in the manner in which dextran based macromolecular crowding agents influence the serum protein.
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Affiliation(s)
- Saikat Biswas
- Department of Chemistry
- Indian Institute of Technology Delhi
- New Delhi 110016
- India
| | - Pramit K. Chowdhury
- Department of Chemistry
- Indian Institute of Technology Delhi
- New Delhi 110016
- India
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What macromolecular crowding can do to a protein. Int J Mol Sci 2014; 15:23090-140. [PMID: 25514413 PMCID: PMC4284756 DOI: 10.3390/ijms151223090] [Citation(s) in RCA: 355] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 01/17/2023] Open
Abstract
The intracellular environment represents an extremely crowded milieu, with a limited amount of free water and an almost complete lack of unoccupied space. Obviously, slightly salted aqueous solutions containing low concentrations of a biomolecule of interest are too simplistic to mimic the “real life” situation, where the biomolecule of interest scrambles and wades through the tightly packed crowd. In laboratory practice, such macromolecular crowding is typically mimicked by concentrated solutions of various polymers that serve as model “crowding agents”. Studies under these conditions revealed that macromolecular crowding might affect protein structure, folding, shape, conformational stability, binding of small molecules, enzymatic activity, protein-protein interactions, protein-nucleic acid interactions, and pathological aggregation. The goal of this review is to systematically analyze currently available experimental data on the variety of effects of macromolecular crowding on a protein molecule. The review covers more than 320 papers and therefore represents one of the most comprehensive compendia of the current knowledge in this exciting area.
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49
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Combined effect of confinement and affinity of crowded environment on conformation switching of adenylate kinase. J Mol Model 2014; 20:2530. [DOI: 10.1007/s00894-014-2530-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 11/12/2014] [Indexed: 01/25/2023]
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Mittal S, Singh LR. Macromolecular crowding decelerates aggregation of a β-rich protein, bovine carbonic anhydrase: a case study. J Biochem 2014; 156:273-82. [PMID: 24917682 DOI: 10.1093/jb/mvu039] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The majority of in vitro investigations concerning protein aggregation have been performed in dilute systems, which poorly reflect the crowded in vivo scenario. Cell interior is highly crowded with soluble and insoluble macromolecules that alter macromolecular properties. Macromolecular crowding is known to enhance the rate and/or extent of protein aggregation. However, most of the understandings were derived from studies with α-rich or predominantly α-proteins. Indeed, α-proteins fold faster than β-proteins and conversion of α-helices to cross β-sheets are responsible for aggregate/amyloid formation. Therefore, it is important to investigate how macromolecular crowding affects the aggregation propensity of β-rich proteins. In this study, we investigated the effect of synthetic macromolecular crowders on bovine carbonic anhydrase (BCA, a β-rich protein) aggregation. In contrast to the effect of macromolecular crowding on α-rich proteins, BCA aggregation was observed to be reduced due to decrease in the population of aggregation-prone intermediates as a consequence of increased native state stability. In addition, the extent of aggregation was found to depend on the nature of the crowder under consideration. Combining the published data on α-proteins and this study, we conclude that macromolecular crowding can have opposite consequences on protein aggregation process depending on the fold type of the protein.
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Affiliation(s)
- Shruti Mittal
- Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi, North Campus, New Delhi 110 007, India
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