1
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Zhang N, Guan W, Cui S, Ai N. Crowded environments tune the fold-switching in metamorphic proteins. Commun Chem 2023; 6:117. [PMID: 37291449 PMCID: PMC10250422 DOI: 10.1038/s42004-023-00909-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/22/2023] [Indexed: 06/10/2023] Open
Abstract
Metamorphic proteins such as circadian clock protein KaiB and human chemokine XCL1 play vital roles in regulating biological processes, including gene expression, circadian clock and innate immune responses, and perform distinct functions in living cell by switching different structures in response to cellular environment stimuli. However, it is unclear how complex and crowded intracellular environments affect conformational rearrangement of metamorphic proteins. Here, the kinetics and thermodynamics of two well-characterized metamorphic proteins, circadian clock protein KaiB and human chemokine XCL1, were quantified in physiologically relevant environments by using NMR spectroscopy, indicating that crowded agents shift equilibrium towards the inactive form (ground-state KaiB and Ltn10-like state XCL1) without disturbing the corresponding structures, and crowded agents have predominantly impact on the exchange rate of XCL1 that switches folds on timescales of seconds, but have slightly impact on the exchange rate of KaiB that switches folds on timescales of hours. Our data shed light on how metamorphic proteins can respond immediately to the changed crowded intracellular conditions that induced by environmental cues and then execute different functions in living cell, and it also enhances our understanding of how environments enrich the sequence-structure-function paradigm.
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Affiliation(s)
- Ning Zhang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- Shandong Energy Institute, Qingdao, 266101, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China.
| | - Wenyan Guan
- Materials and Biomaterials Science and Engineering, University of California, Merced, CA, 95343, USA
| | - Shouqi Cui
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Nana Ai
- Materials and Biomaterials Science and Engineering, University of California, Merced, CA, 95343, USA
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2
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Shet SM, Bharadwaj P, Bisht M, Pereira MM, Thayallath SK, Lokesh V, Franklin G, Kotrappanavar NS, Mondal D. Presenting B-DNA as macromolecular crowding agent to improve efficacy of cytochrome c under various stresses. Int J Biol Macromol 2022; 215:184-191. [PMID: 35716795 DOI: 10.1016/j.ijbiomac.2022.06.093] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/05/2022] [Accepted: 06/12/2022] [Indexed: 11/05/2022]
Abstract
Existence of numerous biomolecules results in biological fluids to be extremely crowded. Thus, Macromolecular crowding is an essential phenomenon to sustain active conformation of proteins in biological systems. Herein, double helical deoxyribonucleic acid (B-DNA) is presented for the first time as a biomacromolecular crowding system for sustainable packaging of cytochrome c (Cyt C). The peroxidase activity of Cyt C was investigated in the presence of various concentrations of B-DNA (from salmon milt). At an optimized concentration of 0.125 mg/mL B-DNA, an 11-fold higher catalytic activity was found than in native Cyt C with improved stability. Molecular docking and spectroscopic analyses revealed that electrostatic and H-bonding are the main interactions between DNA and Cyt C that affect the structural stability and activity of the protein. Moreover, the catalytic activity and stability of the protein were further investigated in the presence of severe process conditions by UV-visible, circular dichroism, and Fourier-transform infrared spectroscopies. Molecularly crowded Cyt C showed significantly higher activity and stability under severe environments such as high temperature (110 °C), oxidative stress, high pH (pH 10) and biological (trypsin) and chemical denaturants (urea) compared to bare Cyt C. The observed results support the suitability of DNA-based macromolecular crowding media as a viable and effective stabilizer of proteins against multiple stresses.
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Affiliation(s)
- Sachin M Shet
- Centre for Nano and Material Sciences, Jain University, Bangalore 562112, India
| | - Pranav Bharadwaj
- Centre for Nano and Material Sciences, Jain University, Bangalore 562112, India
| | - Meena Bisht
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Matheus M Pereira
- Departamento de Química, CICECO, Universidade de Aveiro, Aveiro 3810-193, Portugal
| | | | - Veeresh Lokesh
- Institute of Plant Genetics (IPG), Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
| | - Gregory Franklin
- Institute of Plant Genetics (IPG), Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
| | | | - Dibyendu Mondal
- Centre for Nano and Material Sciences, Jain University, Bangalore 562112, India; Institute of Plant Genetics (IPG), Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland.
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3
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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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4
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Denton AR, Davis WJ. Influence of solvent quality on depletion potentials in colloid-polymer mixtures. J Chem Phys 2021; 155:084904. [PMID: 34470346 DOI: 10.1063/5.0061370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
As first explained by the classic Asakura-Oosawa (AO) model, effective attractive forces between colloidal particles induced by depletion of nonadsorbing polymers can drive demixing of colloid-polymer mixtures into colloid-rich and colloid-poor phases, with practical relevance for purification of water, stability of foods and pharmaceuticals, and macromolecular crowding in biological cells. By idealizing polymer coils as effective penetrable spheres, the AO model qualitatively captures the influence of polymer depletion on thermodynamic phase behavior of colloidal suspensions. In previous work, we extended the AO model to incorporate aspherical polymer conformations and showed that fluctuating shapes of random-walk coils can significantly modify depletion potentials [W. K. Lim and A. R. Denton, Soft Matter 12, 2247 (2016); J. Chem. Phys. 144, 024904 (2016)]. We further demonstrated that the shapes of polymers in crowded environments sensitively depend on solvent quality [W. J. Davis and A. R. Denton, J. Chem. Phys. 149, 124901 (2018)]. Here, we apply Monte Carlo simulation to analyze the influence of solvent quality on depletion potentials in mixtures of hard-sphere colloids and nonadsorbing polymer coils, modeled as ellipsoids whose principal radii fluctuate according to random-walk statistics. We consider both self-avoiding and non-self-avoiding random walks, corresponding to polymers in good and theta solvents, respectively. Our simulation results demonstrate that depletion of polymers of equal molecular weight induces much stronger attraction between colloids in good solvents than in theta solvents and confirm that depletion interactions are significantly influenced by aspherical polymer conformations.
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Affiliation(s)
- Alan R Denton
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108-6050, USA
| | - Wyatt J Davis
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108-6050, USA
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5
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Horvath I, Kumar R, Wittung-Stafshede P. Macromolecular crowding modulates α-synuclein amyloid fiber growth. Biophys J 2021; 120:3374-3381. [PMID: 34242594 PMCID: PMC8391083 DOI: 10.1016/j.bpj.2021.06.032] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/31/2021] [Accepted: 06/28/2021] [Indexed: 11/18/2022] Open
Abstract
The crowdedness of living cells, hundreds of milligrams per milliliter of macromolecules, may affect protein folding, function, and misfolding. Still, such processes are most often studied in dilute solutions in vitro. To assess consequences of the in vivo milieu, we here investigated the effects of macromolecular crowding on the amyloid fiber formation reaction of α-synuclein, the amyloidogenic protein in Parkinson's disease. For this, we performed spectroscopic experiments probing individual steps of the reaction as a function of the macromolecular crowding agent Ficoll70, which is an inert sucrose-based polymer that provides excluded-volume effects. The experiments were performed at neutral pH at quiescent conditions to avoid artifacts due to shaking and glass beads (typical conditions for α-synuclein), using amyloid fiber seeds to initiate reactions. We find that both primary nucleation and fiber elongation steps during α-synuclein amyloid formation are accelerated by the presence of 140 and 280 mg/mL Ficoll70. Moreover, in the presence of Ficoll70 at neutral pH, secondary nucleation appears favored, resulting in faster overall α-synuclein amyloid formation. In contrast, sucrose, a small-molecule osmolyte and building block of Ficoll70, slowed down α-synuclein amyloid formation. The ability of cell environments to modulate reaction kinetics to a large extent, such as severalfold faster individual steps in α-synuclein amyloid formation, is an important consideration for biochemical reactions in living systems.
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Affiliation(s)
- Istvan Horvath
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ranjeet Kumar
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Pernilla Wittung-Stafshede
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
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6
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Köhn B, Kovermann M. All atom insights into the impact of crowded environments on protein stability by NMR spectroscopy. Nat Commun 2020; 11:5760. [PMID: 33188202 PMCID: PMC7666220 DOI: 10.1038/s41467-020-19616-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 10/23/2020] [Indexed: 01/16/2023] Open
Abstract
The high density of macromolecules affecting proteins due to volume exclusion has been discussed in theory but numerous in vivo experiments cannot be sufficiently understood taking only pure entropic stabilization into account. Here, we show that the thermodynamic stability of a beta barrel protein increases equally at all atomic levels comparing crowded environments with dilute conditions by applying multidimensional high-resolution NMR spectroscopy in a systematic manner. Different crowding agents evoke a pure stabilization cooperatively and do not disturb the surface or integrity of the protein fold. The here developed methodology provides a solid base that can be easily expanded to incorporate e.g. binding partners to recognize functional consequences of crowded conditions. Our results are relevant to research projects targeting soluble proteins in vivo as it can be anticipated that their thermodynamic stability increase comparably and has consequently to be taken into account to coherently understand intracellular processes.
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Affiliation(s)
- Birgit Köhn
- Department of Chemistry, University of Konstanz, Universitätsstrasse. 10, 78457, Konstanz, Germany
- Konstanz Research School Chemical Biology KoRS-CB, University of Konstanz, Universitätsstrasse. 10, 78457, Konstanz, Germany
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, Universitätsstrasse. 10, 78457, Konstanz, Germany.
- Konstanz Research School Chemical Biology KoRS-CB, University of Konstanz, Universitätsstrasse. 10, 78457, Konstanz, Germany.
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7
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Perez CP, Elmore DE, Radhakrishnan ML. Computationally Modeling Electrostatic Binding Energetics in a Crowded, Dynamic Environment: Physical Insights from a Peptide–DNA System. J Phys Chem B 2019; 123:10718-10734. [DOI: 10.1021/acs.jpcb.9b09478] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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8
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Adams LM, Andrews RJ, Hu QH, Schmit HL, Hati S, Bhattacharyya S. Crowder-Induced Conformational Ensemble Shift in Escherichia coli Prolyl-tRNA Synthetase. Biophys J 2019; 117:1269-1284. [PMID: 31542226 PMCID: PMC6818166 DOI: 10.1016/j.bpj.2019.08.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/27/2019] [Accepted: 08/28/2019] [Indexed: 01/08/2023] Open
Abstract
The effect of molecular crowding on the structure and function of Escherichia coli prolyl-transfer RNA synthetase (Ec ProRS), a member of the aminoacyl-transfer RNA synthetase family, has been investigated using a combined experimental and theoretical method. Ec ProRS is a multidomain enzyme; coupled-domain dynamics are essential for efficient catalysis. To gain insight into the mechanistic detail of the crowding effect, kinetic studies were conducted with varying concentrations and sizes of crowders. In parallel, spectroscopic and quantum chemical studies were employed to probe the "soft interactions" between crowders and protein side chains. Finally, the dynamics of the dimeric protein was examined in the presence of crowders using a long-duration (70 ns) classical molecular dynamic simulations. The results of the simulations revealed a shift in the conformational ensemble, which is consistent with the preferential exclusion of cosolutes. The "soft interactions" model of the crowding effect also explained the alteration in kinetic parameters. In summary, the study found that the effects of molecular crowding on both conformational dynamics and catalytic function are correlated in the multidomain Ec ProRS, an enzyme that is central to protein synthesis in all living cells. This study affirmed that large and small cosolutes have considerable impacts on the structure, dynamics, and function of modular proteins and therefore must be considered for stabilizing protein-based pharmaceuticals and industrial enzymes.
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Affiliation(s)
- Lauren M Adams
- Department of Chemistry, University of Wisconsin at Eau Claire, Eau Claire, Wisconsin
| | - Ryan J Andrews
- Department of Chemistry, University of Wisconsin at Eau Claire, Eau Claire, Wisconsin
| | - Quin H Hu
- Department of Chemistry, University of Wisconsin at Eau Claire, Eau Claire, Wisconsin
| | - Heidi L Schmit
- Department of Chemistry, University of Wisconsin at Eau Claire, Eau Claire, Wisconsin
| | - Sanchita Hati
- Department of Chemistry, University of Wisconsin at Eau Claire, Eau Claire, Wisconsin.
| | - Sudeep Bhattacharyya
- Department of Chemistry, University of Wisconsin at Eau Claire, Eau Claire, Wisconsin.
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9
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Ostrowska N, Feig M, Trylska J. Modeling Crowded Environment in Molecular Simulations. Front Mol Biosci 2019; 6:86. [PMID: 31572730 PMCID: PMC6749006 DOI: 10.3389/fmolb.2019.00086] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/27/2019] [Indexed: 01/09/2023] Open
Abstract
Biomolecules perform their various functions in living cells, namely in an environment that is crowded by many macromolecules. Thus, simulating the dynamics and interactions of biomolecules should take into account not only water and ions but also other binding partners, metabolites, lipids and macromolecules found in cells. In the last decade, research on how to model macromolecular crowders around proteins in order to simulate their dynamics in models of cellular environments has gained a lot of attention. In this mini-review we focus on the models of crowding agents that have been used in computer modeling studies of proteins and peptides, especially via molecular dynamics simulations.
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Affiliation(s)
- Natalia Ostrowska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland.,College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
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10
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Guin D, Gruebele M. Weak Chemical Interactions That Drive Protein Evolution: Crowding, Sticking, and Quinary Structure in Folding and Function. Chem Rev 2019; 119:10691-10717. [PMID: 31356058 DOI: 10.1021/acs.chemrev.8b00753] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In recent years, better instrumentation and greater computing power have enabled the imaging of elusive biomolecule dynamics in cells, driving many advances in understanding the chemical organization of biological systems. The focus of this Review is on interactions in the cell that affect both biomolecular stability and function and modulate them. The same protein or nucleic acid can behave differently depending on the time in the cell cycle, the location in a specific compartment, or the stresses acting on the cell. We describe in detail the crowding, sticking, and quinary structure in the cell and the current methods to quantify them both in vitro and in vivo. Finally, we discuss protein evolution in the cell in light of current biophysical evidence. We describe the factors that drive protein evolution and shape protein interaction networks. These interactions can significantly affect the free energy, ΔG, of marginally stable and low-population proteins and, due to epistasis, direct the evolutionary pathways in an organism. We finally conclude by providing an outlook on experiments to come and the possibility of collaborative evolutionary biology and biophysical efforts.
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Affiliation(s)
- Drishti Guin
- Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States
| | - Martin Gruebele
- Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States.,Department of Physics , University of Illinois , Urbana , Illinois 61801 , United States.,Center for Biophysics and Quantitative Biology , University of Illinois , Urbana , Illinois 61801 , United States
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11
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Li J, Zheng H, Feng C. Effect of Macromolecular Crowding on the FMN-Heme Intraprotein Electron Transfer in Inducible NO Synthase. Biochemistry 2019; 58:3087-3096. [PMID: 31251033 DOI: 10.1021/acs.biochem.9b00193] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Previous biochemical studies of nitric oxide synthase enzymes (NOSs) were conducted in diluted solutions. However, the intracellular milieu where the proteins perform their biological functions is crowded with macromolecules. The effect of crowding on the electron transfer kinetics of multidomain proteins is much less understood. Herein, we investigated the effect of macromolecular crowding on the FMN-heme intraprotein interdomain electron transfer (IET), an obligatory step in NOS catalysis. A noticeable increase in the IET rate in the bidomain oxygenase/FMN (oxyFMN) and the holoprotein of human inducible NOS (iNOS) was observed upon addition of Ficoll 70 in a nonsaturable manner. Additionally, the magnitude of IET enhancement for the holoenzyme is much higher than that that of the oxyFMN construct. The crowding effect is also evident at different ionic strengths. Importantly, the enhancing extent is similar for the iNOS oxyFMN protein with added Ficoll 70 and Dextran 70 that give the same solution viscosity, showing that specific interactions do not exist between the NOS protein and the crowder. Moreover, the population of the docked FMN-heme state is significantly increased upon addition of Ficoll 70 and the fluorescence lifetime values do not correspond to those in the absence of Ficoll 70. The steady-state cytochrome c reduction by the holoenzyme is noticeably enhanced by the crowder, while the ferricyanide reduction is unchanged. The NO production activity of the iNOS holoenzyme is stimulated by Ficoll 70. The effect of macromolecular crowding on the kinetics can be rationalized on the basis of the excluded volume effect, with an entropic origin. The intraprotein electron transfer kinetics, fluorescence lifetime, and steady-state enzymatic activity results indicate that macromolecular crowding modulates the NOS electron transfer through multiple pathways. Such a mechanism should be applicable to electron transfer in other multidomain redox proteins.
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Affiliation(s)
- Jinghui Li
- College of Pharmacy , University of New Mexico , Albuquerque , New Mexico 87131 , United States
| | - Huayu Zheng
- College of Pharmacy , University of New Mexico , Albuquerque , New Mexico 87131 , United States.,Department of Chemistry and Chemical Biology , University of New Mexico , Albuquerque , New Mexico 87131 , United States
| | - Changjian Feng
- College of Pharmacy , University of New Mexico , Albuquerque , New Mexico 87131 , United States.,Department of Chemistry and Chemical Biology , University of New Mexico , Albuquerque , New Mexico 87131 , United States
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12
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Bhakuni K, Bisht M, Venkatesu P, Mondal D. Designing biological fluid inspired molecularly crowded ionic liquid media as a sustainable packaging platform for cytochrome c. Chem Commun (Camb) 2019; 55:5747-5750. [DOI: 10.1039/c9cc02340b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The present study demonstrated biological fluid inspired design of molecularly crowded IL media and disclosed an innovative and sustainable way for the packaging of Cyt c with enhanced activity and stability.
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Affiliation(s)
| | - Meena Bisht
- Department of Chemistry
- University of Delhi
- India
- Departamento de Química
- Universidade de Aveiro
| | | | - Dibyendu Mondal
- Centre for Nano & Material Sciences
- JAIN (deemed to be University)
- Jain Global Campus
- Bangalore-562112
- India
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13
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Davis WJ, Denton AR. Influence of solvent quality on conformations of crowded polymers. J Chem Phys 2018; 149:124901. [PMID: 30278673 DOI: 10.1063/1.5043434] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The structure and function of polymers in confined environments, e.g., biopolymers in the cytoplasm of a cell, are strongly affected by macromolecular crowding. To explore the influence of solvent quality on conformations of crowded polymers, we model polymers as penetrable ellipsoids, whose shape fluctuations are governed by the statistics of self-avoiding walks, appropriate for a polymer in a good solvent. Within this coarse-grained model, we perform Monte Carlo simulations of mixtures of polymers and hard-nanosphere crowders, including trial changes in polymer size and shape. Penetration of polymers by crowders is incorporated via a free energy cost predicted by polymer field theory. To analyze the impact of crowding on polymer conformations in different solvents, we compute the average polymer shape distributions, radius of gyration, volume, and asphericity over ranges of the polymer-to-crowder size ratio and crowder volume fraction. The simulation results are accurately predicted by a free-volume theory of polymer crowding. Comparison of results for polymers in good and theta solvents indicates that excluded-volume interactions between polymer segments significantly affect crowding, especially in the limit of crowders much smaller than polymers. Our approach may help to motivate future experimental studies of polymers in crowded environments, with possible relevance for drug delivery and gene therapy.
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Affiliation(s)
- Wyatt J Davis
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108-6050, USA
| | - Alan R Denton
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108-6050, USA
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14
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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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15
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Chen E, Esquerra RM, Meléndez PA, Chandrasekaran SS, Kliger DS. Microviscosity in E. coli Cells from Time-Resolved Linear Dichroism Measurements. J Phys Chem B 2018; 122:11381-11389. [PMID: 30118225 DOI: 10.1021/acs.jpcb.8b07362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A protein's folding or function depends on its mobility through the viscous environment that is defined by the presence of macromolecules throughout the cell. The relevant parameter for this mobility is microviscosity-the viscosity on a time and distance scale that is important for protein folding/function movements. A quasi-null, ultrasensitive time-resolved linear dichroism (TRLD) spectroscopy is proving to be a useful tool for measurements of viscosity on this scale, with previous in vitro studies reporting on the microviscosities of crowded environments mimicked by high concentrations of different macromolecules. This study reports the microviscosity experienced by myoglobin in the E. coli cell's heterogeneous cytoplasm by using TRLD to measure rotational diffusion times. The results show that photolyzed deoxyMb ensembles randomize through environment-dependent rotational diffusion with a lifetime of 34 ± 6 ns. This value corresponds to a microviscosity of 2.82 ± 0.42 cP, which is consistent with previous reports of cytoplasmic viscosity in E. coli. The results of these TRLD studies in E. coli (1) provide a measurement of myoglobin mobility in the cytoplasm, (2) taken together with in vitro TRLD studies yield new insights into the nature of the cytoplasmic environment in cells, and (3) demonstrate the feasibility of TRLD as a probe of intracellular viscosity.
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Affiliation(s)
- Eefei Chen
- Department of Chemistry and Biochemistry , University of California , Santa Cruz , California 95064 , United States
| | - Raymond M Esquerra
- Department of Chemistry and Biochemistry , San Francisco State University , San Francisco , California 94132 , United States
| | - Philipp A Meléndez
- Department of Chemistry and Biochemistry , San Francisco State University , San Francisco , California 94132 , United States
| | - Sita S Chandrasekaran
- Department of Chemistry and Biochemistry , San Francisco State University , San Francisco , California 94132 , United States
| | - David S Kliger
- Department of Chemistry and Biochemistry , University of California , Santa Cruz , California 95064 , United States
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16
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Lee HB, Cong A, Leopold H, Currie M, Boersma AJ, Sheets ED, Heikal AA. Rotational and translational diffusion of size-dependent fluorescent probes in homogeneous and heterogeneous environments. Phys Chem Chem Phys 2018; 20:24045-24057. [DOI: 10.1039/c8cp03873b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Macromolecular crowding effects on diffusion depend on the fluorophore structure, the concentration of crowding agents, and the technique employed.
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Affiliation(s)
- Hong Bok Lee
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
| | - Anh Cong
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
| | - Hannah Leopold
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
| | - Megan Currie
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
| | | | - Erin D. Sheets
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
| | - Ahmed A. Heikal
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
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17
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Chen E, Kliger DS. Time-Resolved Linear Dichroism Measurements of Carbonmonoxy Myoglobin as a Probe of the Microviscosity in Crowded Environments. J Phys Chem B 2017; 121:7064-7074. [PMID: 28703591 DOI: 10.1021/acs.jpcb.7b04107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The distribution of viscosities in living cells is heterogeneous because of the different sizes and natures of macromolecular components. When thinking about protein folding/function processes in such an environment, the relevant (micro)viscosity at the micrometer length scale is necessarily distinguished from the bulk (macro)viscosity. The concentration dependencies of microviscosities are determined by a number of factors, such as electrostatic interactions, van der Waals forces, and excluded volume effects. To explore such factors, the rotational diffusion time of myoglobin in the presence of varying concentrations of macromolecules that differ in molecular weight (dextran 6000, 10 000, and 70 000), shape (dextran versus Ficoll), size, and surface charge is measured with time-resolved linear dichroism spectroscopy. The results of these studies offer simple empirically determined linear and exponential functions useful for predicting microviscosities as a function of concentration for these macromolecular crowders that are typically used to study crowding effects on protein folding. To understand how relevant these microviscosity measurements are to intracellular environments, the TRLD results are discussed in the context of studies that measure viscosity in cells.
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Affiliation(s)
- Eefei Chen
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - David S Kliger
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
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18
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Gorensek-Benitez AH, Smith AE, Stadmiller SS, Perez Goncalves GM, Pielak GJ. Cosolutes, Crowding, and Protein Folding Kinetics. J Phys Chem B 2017; 121:6527-6537. [PMID: 28605189 PMCID: PMC5982521 DOI: 10.1021/acs.jpcb.7b03786] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Long accepted as the most important interaction, recent work shows that steric repulsions alone cannot explain the effects of macromolecular cosolutes on the equilibrium thermodynamics of protein stability. Instead, chemical interactions have been shown to modulate, and even dominate, crowding-induced steric repulsions. Here, we use 19F NMR to examine the effects of small and large cosolutes on the kinetics of protein folding and unfolding using the metastable 7 kDa N-terminal SH3 domain of the Drosophila signaling protein drk (SH3), which folds by a two-state mechanism. The small cosolutes consist of trimethylamine N-oxide and sucrose, which increase equilibrium protein stability, and urea, which destabilizes proteins. The macromolecules comprise the stabilizing sucrose polymer, Ficoll, and the destabilizing globular protein, lysozyme. We assessed the effects of these cosolutes on the differences in free energy between the folded state and the transition state and between the unfolded ensemble and the transition state. We then examined the temperature dependence to assess changes in activation enthalpy and entropy. The enthalpically mediated effects are more complicated than suggested by equilibrium measurements. We also observed enthalpic effects with the supposedly inert sucrose polymer, Ficoll, that arise from its macromolecular nature. Assessment of activation entropies shows important contributions from solvent and cosolute, in addition to the configurational entropy of the protein that, again, cannot be gleaned from equilibrium data. Comparing the effects of Ficoll to those of the more physiologically relevant cosolute lysozyme reveals that synthetic polymers are not appropriate models for understanding the kinetics of protein folding in cells.
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Affiliation(s)
| | - Austin E. Smith
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Samantha S. Stadmiller
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | | | - Gary J. Pielak
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, United States
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19
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Abriata LA, Spiga E, Peraro MD. Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics. Biophys J 2017; 111:743-755. [PMID: 27558718 DOI: 10.1016/j.bpj.2016.07.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/06/2016] [Accepted: 07/05/2016] [Indexed: 12/20/2022] Open
Abstract
Most studies of protein structure and function are performed in dilute conditions, but proteins typically experience high solute concentrations in their physiological scenarios and biotechnological applications. High solute concentrations have well-known effects on coarse protein traits like stability, diffusion, and shape, but likely also perturb other traits through finer effects pertinent at the residue and atomic levels. Here, NMR and molecular dynamics investigations on ubiquitin disclose variable interactions with concentrated solutes that lead to localized perturbations of the protein's surface, hydration, electrostatics, and dynamics, all dependent on solute size and chemical properties. Most strikingly, small polar uncharged molecules are sticky on the protein surface, whereas charged small molecules are not, but the latter still perturb the internal protein electrostatics as they diffuse nearby. Meanwhile, interactions with macromolecular crowders are favored mainly through hydrophobic, but not through polar, surface patches. All the tested small solutes strongly slow down water exchange at the protein surface, whereas macromolecular crowders do not exert such strong perturbation. Finally, molecular dynamics simulations predict that unspecific interactions slow down microsecond- to millisecond-timescale protein dynamics despite having only mild effects on pico- to nanosecond fluctuations as corroborated by NMR. We discuss our results in the light of recent advances in understanding proteins inside living cells, focusing on the physical chemistry of quinary structure and cellular organization, and we reinforce the idea that proteins should be studied in native-like media to achieve a faithful description of their function.
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Affiliation(s)
- Luciano A Abriata
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Enrico Spiga
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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20
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Gtari W, Bey H, Aschi A, Bitri L, Othman T. Impact of macromolecular crowding on structure and properties of pepsin and trypsin. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017; 72:98-105. [DOI: 10.1016/j.msec.2016.11.046] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/24/2016] [Accepted: 11/13/2016] [Indexed: 11/25/2022]
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21
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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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22
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Antony M. S, Jaganathan M, Dhathathreyan A. Viscoelastic phase separation at cytochrome c solution/capsules interface. Colloids Surf A Physicochem Eng Asp 2016. [DOI: 10.1016/j.colsurfa.2016.07.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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Skolnick J. Perspective: On the importance of hydrodynamic interactions in the subcellular dynamics of macromolecules. J Chem Phys 2016; 145:100901. [PMID: 27634243 PMCID: PMC5018002 DOI: 10.1063/1.4962258] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/01/2016] [Indexed: 12/30/2022] Open
Abstract
An outstanding challenge in computational biophysics is the simulation of a living cell at molecular detail. Over the past several years, using Stokesian dynamics, progress has been made in simulating coarse grained molecular models of the cytoplasm. Since macromolecules comprise 20%-40% of the volume of a cell, one would expect that steric interactions dominate macromolecular diffusion. However, the reduction in cellular diffusion rates relative to infinite dilution is due, roughly equally, to steric and hydrodynamic interactions, HI, with nonspecific attractive interactions likely playing rather a minor role. HI not only serve to slow down long time diffusion rates but also cause a considerable reduction in the magnitude of the short time diffusion coefficient relative to that at infinite dilution. More importantly, the long range contribution of the Rotne-Prager-Yamakawa diffusion tensor results in temporal and spatial correlations that persist up to microseconds and for intermolecular distances on the order of protein radii. While HI slow down the bimolecular association rate in the early stages of lipid bilayer formation, they accelerate the rate of large scale assembly of lipid aggregates. This is suggestive of an important role for HI in the self-assembly kinetics of large macromolecular complexes such as tubulin. Since HI are important, questions as to whether continuum models of HI are adequate as well as improved simulation methodologies that will make simulations of more complex cellular processes practical need to be addressed. Nevertheless, the stage is set for the molecular simulations of ever more complex subcellular processes.
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Affiliation(s)
- Jeffrey Skolnick
- Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 950 Atlantic Dr., NW, Atlanta, Georgia 30332, USA
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24
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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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25
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Lim WK, Denton AR. Influence of polymer shape on depletion potentials and crowding in colloid-polymer mixtures. SOFT MATTER 2016; 12:2247-2252. [PMID: 26689367 DOI: 10.1039/c5sm02863a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Depletion-induced interactions between colloids in colloid-polymer mixtures depend in range and strength on size, shape, and concentration of depletants. Crowding by colloids in turn affects shapes of polymer coils, such as biopolymers in biological cells. By simulating hard-sphere colloids and random-walk polymers, modeled as fluctuating ellipsoids, we compute depletion-induced potentials and polymer shape distributions. Comparing results with exact density-functional theory calculations, molecular simulations, and experiments, we show that polymer shape fluctuations play an important role in depletion and crowding phenomena.
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Affiliation(s)
- Wei Kang Lim
- Department of Physics, North Dakota State University, Fargo, ND 58108-6050, USA.
| | - Alan R Denton
- Department of Physics, North Dakota State University, Fargo, ND 58108-6050, USA.
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26
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Lim WK, Denton AR. Depletion-induced forces and crowding in polymer-nanoparticle mixtures: Role of polymer shape fluctuations and penetrability. J Chem Phys 2016; 144:024904. [DOI: 10.1063/1.4939766] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Wei Kang Lim
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108-6050, USA
| | - Alan R. Denton
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108-6050, USA
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27
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Kumar R, Sharma D, Jain R, Kumar S, Kumar R. Role of macromolecular crowding and salt ions on the structural-fluctuation of a highly compact configuration of carbonmonoxycytochrome c. Biophys Chem 2015; 207:61-73. [DOI: 10.1016/j.bpc.2015.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 09/04/2015] [Accepted: 09/06/2015] [Indexed: 11/25/2022]
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28
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Sharma GS, Mittal S, Singh LR. Effect of Dextran 70 on the thermodynamic and structural properties of proteins. Int J Biol Macromol 2015; 79:86-94. [DOI: 10.1016/j.ijbiomac.2015.04.051] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 04/20/2015] [Accepted: 04/22/2015] [Indexed: 01/21/2023]
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29
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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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30
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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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31
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Jaganathan M, Dhathathreyan A. Conformational transitions of cytochrome c in sub-micron-sized capsules at air/buffer interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:11356-11365. [PMID: 25233344 DOI: 10.1021/la5024696] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This work presents the design of sub-micron-sized capsules of Cytochrome c (cyt c) in the range 300-350 nm and the conformational transitions of the protein that occur when the films of these capsules spread at the air/buffer interface are subjected to repeated compression-expansion cycles. Steady state fluorescence, time-resolved fluorescence, and circular dichroic (CD) spectra have been used to study the highly compact native conformation (70% helicity) of the protein in the capsules and its stability has been analyzed using cyclic voltammetry. The capsules have been characterized using zeta sizer and high resolution transmission electron microscopy (HRTEM). Surface concentration-surface pressure (Γ-π) isotherms of the films of the capsules spread at air/buffer interface following compression-expansion show destabilizing effect on cyt c. FTIR and CD spectra of these films skimmed from the surface show that the protein transitions gradually from its native helical to an anomalous beta sheet aggregated state. This results from a competition between stabilizing hydrated polar segments of the protein in the capsule and destabilizing nonspecific hydrophobic interactions arising at the air/buffer interface. This 2D model could further our understanding of the spatial and temporal roles of proteins in confined spaces and also in the design of new drug delivery vehicles using proteins.
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32
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Lim WK, Denton AR. Polymer crowding and shape distributions in polymer-nanoparticle mixtures. J Chem Phys 2014; 141:114909. [DOI: 10.1063/1.4895612] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Wei Kang Lim
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108-6050, USA
| | - Alan R. Denton
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108-6050, USA
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33
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Chapanian R, Kwan DH, Constantinescu I, Shaikh FA, Rossi NAA, Withers SG, Kizhakkedathu JN. Enhancement of biological reactions on cell surfaces via macromolecular crowding. Nat Commun 2014; 5:4683. [PMID: 25140641 PMCID: PMC4978540 DOI: 10.1038/ncomms5683] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 07/11/2014] [Indexed: 12/18/2022] Open
Abstract
The reaction of macromolecules such as enzymes and antibodies with cell surfaces is often an inefficient process, requiring large amounts of expensive reagent. Here we report a general method based on macromolecular crowding with a range of neutral polymers to enhance such reactions, using red blood cells (RBCs) as a model system. Rates of conversion of type A and B red blood cells to universal O type by removal of antigenic carbohydrates with selective glycosidases are increased up to 400-fold in the presence of crowders. Similar enhancements are seen for antibody binding. We further explore the factors underlying these enhancements using confocal microscopy and fluorescent recovery after bleaching (FRAP) techniques with various fluorescent protein fusion partners. Increased cell-surface concentration due to volume exclusion, along with two-dimensionally confined diffusion of enzymes close to the cell surface, appear to be the major contributing factors.
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Affiliation(s)
- Rafi Chapanian
- 1] Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Life Sciences Centre, Vancouver, British Columbia, Canada V6T 1Z3 [2] Department of Pathology and Laboratory Medicine, University of British Columbia, 2350 Health Sciences Mall, Life Sciences Centre, Vancouver, British Columbia, Canada V6T 1Z3
| | - David H Kwan
- 1] Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1 [2] Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Iren Constantinescu
- Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Life Sciences Centre, Vancouver, British Columbia, Canada V6T 1Z3
| | - Fathima A Shaikh
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
| | - Nicholas A A Rossi
- Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Life Sciences Centre, Vancouver, British Columbia, Canada V6T 1Z3
| | - Stephen G Withers
- 1] Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1 [2] Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3 [3] Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Jayachandran N Kizhakkedathu
- 1] Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Life Sciences Centre, Vancouver, British Columbia, Canada V6T 1Z3 [2] Department of Pathology and Laboratory Medicine, University of British Columbia, 2350 Health Sciences Mall, Life Sciences Centre, Vancouver, British Columbia, Canada V6T 1Z3 [3] Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
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34
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The effect of macromolecular crowding on the electrostatic component of barnase-barstar binding: a computational, implicit solvent-based study. PLoS One 2014; 9:e98618. [PMID: 24915485 PMCID: PMC4051634 DOI: 10.1371/journal.pone.0098618] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 05/05/2014] [Indexed: 02/02/2023] Open
Abstract
Macromolecular crowding within the cell can impact both protein folding and binding. Earlier models of cellular crowding focused on the excluded volume, entropic effect of crowding agents, which generally favors compact protein states. Recently, other effects of crowding have been explored, including enthalpically-related crowder–protein interactions and changes in solvation properties. In this work, we explore the effects of macromolecular crowding on the electrostatic desolvation and solvent-screened interaction components of protein–protein binding. Our simple model enables us to focus exclusively on the electrostatic effects of water depletion on protein binding due to crowding, providing us with the ability to systematically analyze and quantify these potentially intuitive effects. We use the barnase–barstar complex as a model system and randomly placed, uncharged spheres within implicit solvent to model crowding in an aqueous environment. On average, we find that the desolvation free energy penalties incurred by partners upon binding are lowered in a crowded environment and solvent-screened interactions are amplified. At a constant crowder density (fraction of total available volume occupied by crowders), this effect generally increases as the radius of model crowders decreases, but the strength and nature of this trend can depend on the water probe radius used to generate the molecular surface in the continuum model. In general, there is huge variation in desolvation penalties as a function of the random crowder positions. Results with explicit model crowders can be qualitatively similar to those using a lowered “effective” solvent dielectric to account for crowding, although the “best” effective dielectric constant will likely depend on multiple system properties. Taken together, this work systematically demonstrates, quantifies, and analyzes qualitative intuition-based insights into the effects of water depletion due to crowding on the electrostatic component of protein binding, and it provides an initial framework for future analyses.
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35
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Christiansen A, Wittung-Stafshede P. Quantification of excluded volume effects on the folding landscape of Pseudomonas aeruginosa apoazurin in vitro. Biophys J 2014; 105:1689-99. [PMID: 24094410 DOI: 10.1016/j.bpj.2013.08.038] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 08/09/2013] [Accepted: 08/15/2013] [Indexed: 11/15/2022] Open
Abstract
Proteins fold and function inside cells that are crowded with macromolecules. Here, we address the role of the resulting excluded volume effects by in vitro spectroscopic studies of Pseudomonas aeruginosa apoazurin stability (thermal and chemical perturbations) and folding kinetics (chemical perturbation) as a function of increasing levels of crowding agents dextran (sizes 20, 40, and 70 kDa) and Ficoll 70. We find that excluded volume theory derived by Minton quantitatively captures the experimental effects when crowding agents are modeled as arrays of rods. This finding demonstrates that synthetic crowding agents are useful for studies of excluded volume effects. Moreover, thermal and chemical perturbations result in free energy effects by the presence of crowding agents that are identical, which shows that the unfolded state is energetically the same regardless of method of unfolding. This also underscores the two-state approximation for apoazurin's unfolding reaction and suggests that thermal and chemical unfolding experiments can be used in an interchangeable way. Finally, we observe increased folding speed and invariant unfolding speed for apoazurin in the presence of macromolecular crowding agents, a result that points to unfolded-state perturbations. Although the absolute magnitude of excluded volume effects on apoazurin is only on the order of 1-3 kJ/mol, differences of this scale may be biologically significant.
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36
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Crowding in Polymer–Nanoparticle Mixtures. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 307:27-71. [DOI: 10.1016/b978-0-12-800046-5.00003-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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37
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Denatured state structural property determines protein stabilization by macromolecular crowding: a thermodynamic and structural approach. PLoS One 2013; 8:e78936. [PMID: 24265729 PMCID: PMC3827121 DOI: 10.1371/journal.pone.0078936] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 09/26/2013] [Indexed: 11/19/2022] Open
Abstract
Understanding of protein structure and stability gained to date has been acquired through investigations made under dilute conditions where total macromolecular concentration never surpasses 10 g l−1. However, biological macromolecules are known to evolve and function under crowded intracellular environments that comprises of proteins, nucleic acids, ribosomes and carbohydrates etc. Crowded environment is known to result in altered biological properties including thermodynamic, structural and functional aspect of macromolecules as compared to the macromolecules present in our commonly used experimental dilute buffers (for example, Tris HCl or phosphate buffer). In this study, we have investigated the thermodynamic and structural consequences of synthetic crowding agent (Ficoll 70) on three different proteins (Ribonuclease-A, lysozyme and holo α-lactalbumin) at different pH values. We report here that the effect of crowding is protein dependent in terms of protein thermal stability and structure. We also observed that the structural characteristics of the denatured state determines if crowding will have an effect or not on the protein stability.
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38
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Abriata LA, Spiga E, Dal Peraro M. All-atom simulations of crowding effects on ubiquitin dynamics. Phys Biol 2013; 10:045006. [DOI: 10.1088/1478-3975/10/4/045006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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39
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Larini L, Shea JE. Double Resolution Model for Studying TMAO/Water Effective Interactions. J Phys Chem B 2013; 117:13268-77. [DOI: 10.1021/jp403635g] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Luca Larini
- Department of Chemistry
and Biochemistry
and of Physics, University of California, Santa Barbara, Santa Barbara, California 93106, United
States
| | - Joan-Emma Shea
- Department of Chemistry
and Biochemistry
and of Physics, University of California, Santa Barbara, Santa Barbara, California 93106, United
States
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Christiansen A, Wang Q, Cheung MS, Wittung-Stafshede P. Effects of macromolecular crowding agents on protein folding in vitro and in silico. Biophys Rev 2013; 5:137-145. [PMID: 28510156 DOI: 10.1007/s12551-013-0108-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 01/31/2013] [Indexed: 01/24/2023] Open
Abstract
Proteins fold and function inside cells which are environments very different from that of dilute buffer solutions most often used in traditional experiments. The crowded milieu results in excluded-volume effects, increased bulk viscosity and amplified chances for inter-molecular interactions. These environmental factors have not been accounted for in most mechanistic studies of protein folding executed during the last decades. The question thus arises as to how these effects-present when polypeptides normally fold in vivo-modulate protein biophysics. To address excluded volume effects, we use synthetic macromolecular crowding agents, which take up significant volume but do not interact with proteins, in combination with strategically selected proteins and a range of equilibrium and time-resolved biophysical (spectroscopic and computational) methods. In this review, we describe key observations on macromolecular crowding effects on protein stability, folding and structure drawn from combined in vitro and in silico studies. As expected based on Minton's early predictions, many proteins (apoflavodoxin, VlsE, cytochrome c, and S16) became more thermodynamically stable (magnitude depends inversely on protein stability in buffer) and, unexpectedly, for apoflavodoxin and VlsE, the folded states changed both secondary structure content and, for VlsE, overall shape in the presence of macromolecular crowding. For apoflavodoxin and cytochrome c, which have complex kinetic folding mechanisms, excluded volume effects made the folding energy landscapes smoother (i.e., less misfolding and/or kinetic heterogeneity) than in buffer.
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Affiliation(s)
| | - Qian Wang
- Department of Physics, University of Houston, Houston, TX, 77204, USA
| | - Margaret S Cheung
- Department of Physics, University of Houston, Houston, TX, 77204, USA
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