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Xu S, Wang J, Dong J. Nonspecific interaction and overlap concentration influence macromolecular crowding effect on glucose oxidase activity. Int J Biol Macromol 2023; 241:124525. [PMID: 37086776 DOI: 10.1016/j.ijbiomac.2023.124525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 04/14/2023] [Accepted: 04/15/2023] [Indexed: 04/24/2023]
Abstract
Macromolecular crowding can change kinetics of enzyme catalysis. How interaction between enzymes and neighboring macromolecules contributes to the crowding effect on enzyme catalysis has not been quantitatively revealed. In this study, crowding effects of dextran and poly(ethylene glycol) (PEG) on glucose oxidase (GOx) are studied. Fluorescence resonance energy transfer experiments show the high transfer efficiency and stable interaction between the dextran and GOx. Further fluorescence quenching analysis also proves that the association of the dextran-GOx pair can become stronger than that of the PEG-GOx pair. Dextrans with concentrations above or below their chain overlap concentrations (c*) reduce Michaelis constants (Km) of GOx catalysis by 90 % or 45 %, respectively, through volume exclusion mechanism, and in the meantime elevate the enzymatic efficiency (kcat/Km) by 8-fold or by 3-fold, respectively, which is more dramatic than that found in other enzymes before. Strong association between the enzyme and the dextran results in slow turnover rates (kcat). Intermediate crowding with weak to moderate affinity to the enzyme below the c* can tune the kcat higher than in the free state. Catalysis under crowded conditions is a joint effect of the enzyme-crowder nonspecific interaction, volume exclusion and overlap condition of the crowders.
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Affiliation(s)
- Siyuan Xu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, Zhejiang Province 312000, China
| | - Jie Wang
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, Zhejiang Province 312000, China
| | - Jian Dong
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, Zhejiang Province 312000, China.
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2
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Ostrowska N, Feig M, Trylska J. Varying molecular interactions explain aspects of crowder-dependent enzyme function of a viral protease. PLoS Comput Biol 2023; 19:e1011054. [PMID: 37098073 PMCID: PMC10162569 DOI: 10.1371/journal.pcbi.1011054] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 05/05/2023] [Accepted: 03/28/2023] [Indexed: 04/26/2023] Open
Abstract
Biochemical processes in cells, including enzyme-catalyzed reactions, occur in crowded conditions with various background macromolecules occupying up to 40% of cytoplasm's volume. Viral enzymes in the host cell also encounter such crowded conditions as they often function at the endoplasmic reticulum membranes. We focus on an enzyme encoded by the hepatitis C virus, the NS3/4A protease, which is crucial for viral replication. We have previously found experimentally that synthetic crowders, polyethylene glycol (PEG) and branched polysucrose (Ficoll), differently affect the kinetic parameters of peptide hydrolysis catalyzed by NS3/4A. To gain understanding of the reasons for such behavior, we perform atomistic molecular dynamics simulations of NS3/4A in the presence of either PEG or Ficoll crowders and with and without the peptide substrates. We find that both crowder types make nanosecond long contacts with the protease and slow down its diffusion. However, they also affect the enzyme structural dynamics; crowders induce functionally relevant helical structures in the disordered parts of the protease cofactor, NS4A, with the PEG effect being more pronounced. Overall, PEG interactions with NS3/4A are slightly stronger but Ficoll forms more hydrogen bonds with NS3. The crowders also interact with substrates; we find that the substrate diffusion is reduced much more in the presence of PEG than Ficoll. However, contrary to NS3, the substrate interacts more strongly with Ficoll than with PEG crowders, with the substrate diffusion being similar to crowder diffusion. Importantly, crowders also affect the substrate-enzyme interactions. We observe that both PEG and Ficoll enhance the presence of substrates near the active site, especially near catalytic H57 but Ficoll crowders increase substrate binding more than PEG molecules.
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Affiliation(s)
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
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3
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Rastogi H, Chowdhury PK. Understanding enzyme behavior in a crowded scenario through modulation in activity, conformation and dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140699. [PMID: 34298166 DOI: 10.1016/j.bbapap.2021.140699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 01/25/2023]
Abstract
Macromolecular crowding, inside the physiological interior, modulates the energy landscape of biological macromolecules in multiple ways. Amongst these, enzymes occupy a special place and hence understanding the function of the same in the crowded interior is of utmost importance. In this study, we have investigated the manner in which the multidomain enzyme, AK3L1 (PDB ID: 1ZD8), an isoform of adenylate kinase, has its features affected in presence of commonly used crowders (PEG 8, Dextran 40, Dextran 70, and Ficoll 70). Michaelis Menten plots reveal that the crowders in general enhance the activity of the enzyme, with the Km and Vmax values showing significant variations. Ficoll 70, induced the maximum activity for AK3L1 at 100 g/L, beyond which the activity reduced. Ensemble FRET studies were performed to provide insights into the relative domain (LID and CORE) displacements in presence of the crowders. Solvation studies reveal that the protein matrix surrounding the probe CPM (7-diethylamino-3-(4-maleimido-phenyl)-4-methylcoumarin) gets restricted in presence of the crowders, with Ficoll 70 providing the maximum rigidity, the same being linked to the decrease in the activity of the enzyme. Through our multipronged approach, we have observed a distinct correlation between domain displacement, enzyme activity and associated dynamics. Thus, keeping in mind the complex nature of enzyme activity and the surrounding bath of dense soup that the biological entity remains immersed in, indeed more such approaches need to be undertaken to have a better grasp of the "enzymes in the crowd".
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Affiliation(s)
- Harshita Rastogi
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Pramit K Chowdhury
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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4
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Wilcox XE, Chung CB, Slade KM. Macromolecular crowding effects on the kinetics of opposing reactions catalyzed by alcohol dehydrogenase. Biochem Biophys Rep 2021; 26:100956. [PMID: 33665382 PMCID: PMC7905371 DOI: 10.1016/j.bbrep.2021.100956] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 01/03/2021] [Accepted: 02/09/2021] [Indexed: 12/01/2022] Open
Abstract
In order to better understand how the complex, densely packed, heterogeneous milieu of a cell influences enzyme kinetics, we exposed opposing reactions catalyzed by yeast alcohol dehydrogenase (YADH) to both synthetic and protein crowders ranging from 10 to 550 kDa. The results reveal that the effects from macromolecular crowding depend on the direction of the reaction. The presence of the synthetic polymers, Ficoll and dextran, decrease Vmax and Km for ethanol oxidation. In contrast, these crowders have little effect or even increase these kinetic parameters for acetaldehyde reduction. This increase in Vmax is likely due to excluded volume effects, which are partially counteracted by viscosity hindering release of the NAD+ product. Macromolecular crowding is further complicated by the presence of a depletion layer in solutions of dextran larger than YADH, which diminishes the hindrance from viscosity. The disparate effects from 25 g/L dextran or glucose compared to 25 g/L Ficoll or sucrose reveals that soft interactions must also be considered. Data from binary mixtures of glucose, dextran, and Ficoll support this “tuning” of opposing factors. While macromolecular crowding was originally proposed to influence proteins mainly through excluded volume effects, this work compliments the growing body of evidence revealing that other factors, such as preferential hydration, chemical interactions, and the presence of a depletion layer also contribute to the overall effect of crowding. Yeast alcohol dehydrogenase reduction of acetaldehyde is enhanced by crowding. Crowding effects on YADH kinetics depend on the direction of the reaction. Crowders like dextran can be used as a tool to elucidate enzyme mechanism. Excluded volume optimizes YADH hydride transfer; viscosity hinders product release. The presence of a depletion layer with large crowders mitigates their effects.
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Affiliation(s)
- Xander E Wilcox
- Department of Chemistry, University of California at Davis, CA, 95616, USA
| | - Charmaine B Chung
- Department of Chemistry, Hobart and William Smith Colleges, 300 Pulteney St, Geneva, NY, 14456, USA
| | - Kristin M Slade
- Department of Chemistry, Hobart and William Smith Colleges, 300 Pulteney St, Geneva, NY, 14456, USA
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5
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Wang M, Wang A, Li J, Li Q, Bai S. Thermolysin-triggered short peptides self-assembly in confined space and application in cell culturing. Colloids Surf A Physicochem Eng Asp 2020. [DOI: 10.1016/j.colsurfa.2020.125213] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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Popielec A, Ostrowska N, Wojciechowska M, Feig M, Trylska J. Crowded environment affects the activity and inhibition of the NS3/4A protease. Biochimie 2020; 176:169-180. [DOI: 10.1016/j.biochi.2020.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/17/2020] [Accepted: 07/17/2020] [Indexed: 12/18/2022]
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7
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Akella R, Drozdz MA, Humphreys JM, Jiou J, Durbacz MZ, Mohammed ZJ, He H, Liwocha J, Sekulski K, Goldsmith EJ. A Phosphorylated Intermediate in the Activation of WNK Kinases. Biochemistry 2020; 59:1747-1755. [PMID: 32314908 PMCID: PMC7914002 DOI: 10.1021/acs.biochem.0c00146] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
WNK kinases autoactivate by autophosphorylation. Crystallography of the kinase domain of WNK1 phosphorylated on the primary activating site (pWNK1) in the presence of AMP-PNP reveals a well-ordered but inactive configuration. This new pWNK1 structure features specific and unique interactions of the phosphoserine, less hydration, and smaller cavities compared with those of unphosphorylated WNK1 (uWNK1). Because WNKs are activated by osmotic stress in cells, we addressed whether the structure was influenced directly by osmotic pressure. pWNK1 crystals formed in PEG3350 were soaked in the osmolyte sucrose. Suc-WNK1 crystals maintained X-ray diffraction, but the lattice constants and pWNK1 structure changed. Differences were found in the activation loop and helix C, common switch loci in kinase activation. On the basis of these structural changes, we tested for effects on in vitro activity of two WNKs, pWNK1 and pWNK3. The osmolyte PEG400 enhanced ATPase activity. Our data suggest multistage activation of WNKs.
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Affiliation(s)
- Radha Akella
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-8816, USA
| | - Mateusz A. Drozdz
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-8816, USA
| | - John M. Humphreys
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-8816, USA
| | - Jenny Jiou
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-8816, USA
| | - Mateusz Z. Durbacz
- Faculty of Agronomy and Bioengineering, University of Life Sciences, Wojska Polskiego 28, 60-624 Poznan, Poland
| | - Zuhair J. Mohammed
- Biomedical Engineering, University of Texas at Dallas, Richardson, TX 75080
| | - Haixia He
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-8816, USA
| | - Joanna Liwocha
- Department of Molecular Machines and Signaling, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Kamil Sekulski
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-8816, USA
| | - Elizabeth J. Goldsmith
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-8816, USA
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8
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Chu X, Suo Z, Wang J. Confinement and Crowding Effects on Folding of a Multidomain Y-Family DNA Polymerase. J Chem Theory Comput 2020; 16:1319-1332. [PMID: 31972079 PMCID: PMC7258223 DOI: 10.1021/acs.jctc.9b01146] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Proteins in vivo endure highly various interactions from the luxuriant surrounding macromolecular cosolutes. Confinement and macromolecular crowding are the two major effects that should be considered while comparing the results of protein dynamics from in vitro to in vivo. However, efforts have been largely focused on single domain protein folding up to now, and the quantifications of the in vivo effects in terms of confinements and crowders on modulating the structure and dynamics as well as the physical understanding of the underlying mechanisms on multidomain protein folding are still challenging. Here we developed a topology-based model to investigate folding of a multidomain Y-family DNA polymerase (DPO4) within spherical confined space and in the presence of repulsive and attractive crowders. We uncovered that the entropic component of the thermodynamic driving force led by confinements and repulsive crowders increases the stability of folded states relative to the folding intermediates and unfolded states, while the enthalpic component of the thermodynamic driving force led by attractive crowders gives rise to the opposite effects with less stability. We found that the shapes of DPO4 conformations influenced by the confinements and the crowders are quite different even when only the entropic component of the thermodynamic driving force is considered. We uncovered that under all in vivo conditions, the folding cooperativity of DPO4 decreases compared to that in bulk. We showed that the loss of folding cooperativity can promote the sequential domain-wise folding, which was widely found in cotranslational multidomain protein folding, and effectively prohibit the backtracking led by topological frustrations during multidomain protein folding processes.
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Affiliation(s)
- Xiakun Chu
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794, United States
| | - Zucai Suo
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306, United States
| | - Jin Wang
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794, United States
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9
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Sagar A, Svergun D, Bernadó P. Structural Analyses of Intrinsically Disordered Proteins by Small-Angle X-Ray Scattering. Methods Mol Biol 2020; 2141:249-269. [PMID: 32696361 DOI: 10.1007/978-1-0716-0524-0_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Small-angle X-ray scattering (SAXS) is a low-resolution method for the structural characterization of biological macromolecules in solution. Information about the overall structural features provided by SAXS is highly complementary to X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy, which are high-resolution methods. SAXS not only provides the shape, oligomeric state, and quaternary structure of folded proteins and protein complexes but also allows for quantitative analysis of flexible biomolecules. In this chapter, the most relevant SAXS procedures for structural characterization of flexible macromolecules, including intrinsically disordered proteins (IDPs), are presented. The sample requirements for SAXS experiments on protein solutions and the sequence of steps in data collection and processing are described. The use of the advanced data analysis tools to quantitatively characterize flexible proteins is presented in detail. Typical experimental issues and potential problems encountered during SAXS data measurements and analyses are discussed.
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Affiliation(s)
- Amin Sagar
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, France.
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Hamburg, Germany
| | - Pau Bernadó
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, France.
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10
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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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11
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Dolinska MB, Wingfield PT, Young KL, Sergeev YV. The TYRP1-mediated protection of human tyrosinase activity does not involve stable interactions of tyrosinase domains. Pigment Cell Melanoma Res 2019; 32:753-765. [PMID: 31077632 DOI: 10.1111/pcmr.12791] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/15/2019] [Accepted: 05/04/2019] [Indexed: 12/20/2022]
Abstract
Tyrosinases are melanocyte-specific enzymes involved in melanin biosynthesis. Mutations in their genes cause oculocutaneous albinism associated with reduced or altered pigmentation of skin, hair, and eyes. Here, the recombinant human intra-melanosomal domains of tyrosinase, TYRtr (19-469), and tyrosinase-related protein 1, TYRP1tr (25-472), were studied in vitro to define their functional relationship. Proteins were expressed or coexpressed in whole Trichoplusia ni larvae and purified. Their associations were studied using gel filtration and sedimentation equilibrium methods. Protection of TYRtr was studied by measuring the kinetics of tyrosinase diphenol oxidase activity in the presence (1:1 and 1:20 molar ratios) or the absence of TYRP1tr for 10 hr under conditions mimicking melanosomal and ER pH values. Our data indicate that TYRtr incubation with excess TYRP1tr protects TYR, increasing its stability over time. However, this mechanism does not appear to involve the formation of stable hetero-oligomeric complexes to maintain the protective function.
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Affiliation(s)
- Monika B Dolinska
- National Eye Institute, National Institutes of Health, Bethesda, Maryland
| | - Paul T Wingfield
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland
| | - Kenneth L Young
- National Eye Institute, National Institutes of Health, Bethesda, Maryland
| | - Yuri V Sergeev
- National Eye Institute, National Institutes of Health, Bethesda, Maryland
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12
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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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13
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Harigua-Souiai E, Abdelkrim YZ, Bassoumi-Jamoussi I, Zakraoui O, Bouvier G, Essafi-Benkhadir K, Banroques J, Desdouits N, Munier-Lehmann H, Barhoumi M, Tanner NK, Nilges M, Blondel A, Guizani I. Identification of novel leishmanicidal molecules by virtual and biochemical screenings targeting Leishmania eukaryotic translation initiation factor 4A. PLoS Negl Trop Dis 2018; 12:e0006160. [PMID: 29346371 PMCID: PMC5790279 DOI: 10.1371/journal.pntd.0006160] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 01/30/2018] [Accepted: 12/11/2017] [Indexed: 01/25/2023] Open
Abstract
Leishmaniases are neglected parasitic diseases in spite of the major burden they inflict on public health. The identification of novel drugs and targets constitutes a research priority. For that purpose we used Leishmania infantum initiation factor 4A (LieIF), an essential translation initiation factor that belongs to the DEAD-box proteins family, as a potential drug target. We modeled its structure and identified two potential binding sites. A virtual screening of a diverse chemical library was performed for both sites. The results were analyzed with an in-house version of the Self-Organizing Maps algorithm combined with multiple filters, which led to the selection of 305 molecules. Effects of these molecules on the ATPase activity of LieIF permitted the identification of a promising hit (208) having a half maximal inhibitory concentration (IC50) of 150 ± 15 μM for 1 μM of protein. Ten chemical analogues of compound 208 were identified and two additional inhibitors were selected (20 and 48). These compounds inhibited the mammalian eIF4I with IC50 values within the same range. All three hits affected the viability of the extra-cellular form of L. infantum parasites with IC50 values at low micromolar concentrations. These molecules showed non-significant toxicity toward THP-1 macrophages. Furthermore, their anti-leishmanial activity was validated with experimental assays on L. infantum intramacrophage amastigotes showing IC50 values lower than 4.2 μM. Selected compounds exhibited selectivity indexes between 19 to 38, which reflects their potential as promising anti-Leishmania molecules.
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Affiliation(s)
- Emna Harigua-Souiai
- Laboratory of Molecular Epidemiology and Experimental Pathology – LR11IPT04, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, Tunisia
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Yosser Zina Abdelkrim
- Laboratory of Molecular Epidemiology and Experimental Pathology – LR11IPT04, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, Tunisia
- Laboratory of Microbial Gene Expression (EGM), CNRS UMR8261/Université Paris Diderot P7, Sorbonne Paris Cité & PSL, Institut de Biologie Physico-Chimique, Paris, France
- Faculté des Sciences de Bizerte, Université de Carthage, Tunis, Tunisia
| | - Imen Bassoumi-Jamoussi
- Laboratory of Molecular Epidemiology and Experimental Pathology – LR11IPT04, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, Tunisia
| | - Ons Zakraoui
- Laboratory of Molecular Epidemiology and Experimental Pathology – LR11IPT04, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, Tunisia
| | - Guillaume Bouvier
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Khadija Essafi-Benkhadir
- Laboratory of Molecular Epidemiology and Experimental Pathology – LR11IPT04, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, Tunisia
| | - Josette Banroques
- Laboratory of Microbial Gene Expression (EGM), CNRS UMR8261/Université Paris Diderot P7, Sorbonne Paris Cité & PSL, Institut de Biologie Physico-Chimique, Paris, France
| | - Nathan Desdouits
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Hélène Munier-Lehmann
- Institut Pasteur, Unité de Chimie et Biocatalyse, Département de Biologie Structurale et Chimie, Paris, France
- Unité Mixte de Recherche 3523, Centre National de la Recherche Scientifique, Paris, France
| | - Mourad Barhoumi
- Laboratory of Molecular Epidemiology and Experimental Pathology – LR11IPT04, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, Tunisia
| | - N. Kyle Tanner
- Laboratory of Microbial Gene Expression (EGM), CNRS UMR8261/Université Paris Diderot P7, Sorbonne Paris Cité & PSL, Institut de Biologie Physico-Chimique, Paris, France
| | - Michael Nilges
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Arnaud Blondel
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Ikram Guizani
- Laboratory of Molecular Epidemiology and Experimental Pathology – LR11IPT04, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, Tunisia
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14
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Acosta LC, Perez Goncalves GM, Pielak GJ, Gorensek-Benitez AH. Large cosolutes, small cosolutes, and dihydrofolate reductase activity. Protein Sci 2017; 26:2417-2425. [PMID: 28971539 DOI: 10.1002/pro.3316] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/27/2017] [Accepted: 09/27/2017] [Indexed: 11/06/2022]
Abstract
Protein enzymes are the main catalysts in the crowded and complex cellular interior, but their activity is almost always studied in dilute buffered solutions. Studies that attempt to recreate the cellular interior in vitro often utilize synthetic polymers as crowding agents. Here, we report the effects of the synthetic polymer cosolutes Ficoll, dextran, and polyvinylpyrrolidone, and their respective monomers, sucrose, glucose, and 1-ethyl-2-pyrrolidone, on the activity of the 18-kDa monomeric enzyme, Escherichia coli dihydrofolate reductase. At low concentrations, reductase activity increases relative to buffer and monomers, suggesting a macromolecular effect. However, the effect decreases at higher concentrations, approaching, and, in some cases, falling below buffer values. We also assessed activity in terms of volume occupancy, viscosity, and the overlap concentration (where polymers form an interwoven mesh). The trends vary with polymer family, but changes in activity are within threefold of buffer values. We also compiled and analyzed results from previous studies and conclude that alterations of steady-state enzyme kinetics in solutions crowded with synthetic polymers are idiosyncratic with respect to the crowding agent and enzyme.
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Affiliation(s)
| | | | - Gary J Pielak
- Department of Chemistry.,Department of Biochemistry and Biophysics.,Lineberger Comprehensive Cancer Center.,Integrative Program for Biological and Genome Sciences University of North Carolina, Chapel Hill, NC, 27599, USA
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15
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Li J, Xing X, Sun B, Zhao Y, Wu Z. Metallofullerenol Inhibits Cellular Iron Uptake by Inducing Transferrin Tetramerization. Chem Asian J 2017; 12:2646-2651. [PMID: 28815927 DOI: 10.1002/asia.201700910] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/16/2017] [Indexed: 12/24/2022]
Abstract
Herein, A549 tumor cell proliferation was confirmed to be positively dependent on the concentration of Fe3+ or transferrin (Tf). Gd@C82 (OH)22 or C60 (OH)22 effectively inhibited the iron uptake and the subsequent proliferation of A549 cells. The conformational changes of Tf mixed with FeCl3 , GdCl3 , C60 (OH)22 or Gd@C82 (OH)22 were obtained by SAXS. The results demonstrate that Tf homodimers can be decomposed into monomers in the presence of FeCl3 , GdCl3 or C60 (OH)22 , but associated into tetramers in the presence of Gd@C82 (OH)22 . The larger change of SAXS shapes between Tf+C60 (OH)22 and Tf+FeCl3 implies that C60 (OH)22 is bound to Tf, blocking the iron-binding site. The larger deviation of the SAXS shape from a possible crystal structure of Tf tetramer implies that Gd@C82 (OH)22 is bound to the Tf tetramer, thus disturbing iron transport. This study well explains the inhibition mechanism of Gd@C82 (OH)22 and C60 (OH)22 on the iron uptake and the proliferation of A549 tumor cells and highlights the specific interactions of a nanomedicine with the target biomolecules in cancer therapy.
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Affiliation(s)
- Jinxia Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Xueqing Xing
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Baoyun Sun
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Zhonghua Wu
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
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16
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Xu G, Zhao J, Cheng K, Wu Q, Liu X, Liu M, Li C. The Effects of Macromolecular Crowding on Calmodulin Structure and Function. Chemistry 2017; 23:6736-6740. [DOI: 10.1002/chem.201700367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Indexed: 02/07/2023]
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; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P. R. China
| | - Jiajing Zhao
- 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; 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
| | - 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; 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; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P. R. China
| | - Xiaoli 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; 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; 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; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P. R. China
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17
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The molecular choreography of protein synthesis: translational control, regulation, and pathways. Q Rev Biophys 2016; 49:e11. [PMID: 27658712 DOI: 10.1017/s0033583516000056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Translation of proteins by the ribosome regulates gene expression, with recent results underscoring the importance of translational control. Misregulation of translation underlies many diseases, including cancer and many genetic diseases. Decades of biochemical and structural studies have delineated many of the mechanistic details in prokaryotic translation, and sketched the outlines of eukaryotic translation. However, translation may not proceed linearly through a single mechanistic pathway, but likely involves multiple pathways and branchpoints. The stochastic nature of biological processes would allow different pathways to occur during translation that are biased by the interaction of the ribosome with other translation factors, with many of the steps kinetically controlled. These multiple pathways and branchpoints are potential regulatory nexus, allowing gene expression to be tuned at the translational level. As research focus shifts toward eukaryotic translation, certain themes will be echoed from studies on prokaryotic translation. This review provides a general overview of the dynamic data related to prokaryotic and eukaryotic translation, in particular recent findings with single-molecule methods, complemented by biochemical, kinetic, and structural findings. We will underscore the importance of viewing the process through the viewpoints of regulation, translational control, and heterogeneous pathways.
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18
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Wilcox AE, LoConte MA, Slade KM. Effects of Macromolecular Crowding on Alcohol Dehydrogenase Activity Are Substrate-Dependent. Biochemistry 2016; 55:3550-8. [PMID: 27283046 DOI: 10.1021/acs.biochem.6b00257] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enzymes operate in a densely packed cellular environment that rarely matches the dilute conditions under which they are studied. To better understand the ramifications of this crowding, the Michaelis-Menten kinetics of yeast alcohol dehydrogenase (YADH) were monitored spectrophotometrically in the presence of high concentrations of dextran. Crowding decreased the maximal rate of the reaction by 40% for assays with ethanol, the primary substrate of YADH. This observation was attributed to slowed release of the reduced β-nicotinamide adenine dinucleotide product, which is rate-limiting. In contrast, when larger alcohols were used as the YADH substrate, the rate-limiting step becomes hydride transfer and crowding instead increased the maximal rate of the reaction by 20-40%. This work reveals the importance of considering enzyme mechanism when evaluating the ways in which crowding can alter kinetics.
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Affiliation(s)
- A E Wilcox
- Department of Chemistry, Hobart and William Smith Colleges , Geneva, New York 14456, United States
| | - Micaela A LoConte
- Department of Chemistry, Hobart and William Smith Colleges , Geneva, New York 14456, United States
| | - Kristin M Slade
- Department of Chemistry, Hobart and William Smith Colleges , Geneva, New York 14456, United States
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19
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Celaya G, Fernández-Higuero JA, Martin I, Rivas G, Moro F, Muga A. Crowding Modulates the Conformation, Affinity, and Activity of the Components of the Bacterial Disaggregase Machinery. J Mol Biol 2016; 428:2474-2487. [DOI: 10.1016/j.jmb.2016.04.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 04/18/2016] [Accepted: 04/20/2016] [Indexed: 12/13/2022]
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20
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Mikaelsson T, Ådén J, Wittung-Stafshede P, Johansson LBÅ. Macromolecular crowding effects on two homologs of ribosomal protein s16: protein-dependent structural changes and local interactions. Biophys J 2015; 107:401-410. [PMID: 25028882 DOI: 10.1016/j.bpj.2014.05.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 05/28/2014] [Accepted: 05/30/2014] [Indexed: 11/30/2022] Open
Abstract
Proteins function in cellular environments that are crowded with biomolecules, and in this reduced available space, their biophysical properties may differ from those observed in dilute solutions in vitro. Here, we investigated the effects of a synthetic macromolecular crowding agent, dextran 20, on the folded states of hyperthermophilic (S16Thermo) and mesophilic (S16Meso) homologs of the ribosomal protein S16. As expected for an excluded-volume effect, the resistance of the mesophilic protein to heat-induced unfolding increased in the presence of dextran 20, and chemical denaturation experiments at different fixed temperatures showed the macromolecular crowding effect to be temperature-independent. Förster resonance energy transfer experiments show that intramolecular distances between an intrinsic Trp residue and BODIPY-labeled S16Meso depend on the level of the crowding agent. The BODIPY group was attached at three specific positions in S16Meso, allowing measurements of three intraprotein distances. All S16Meso variants exhibited a decrease in the average Trp-BODIPY distance at up to 100 mg/mL dextran 20, whereas the changes in distance became anisotropic (one distance increased, two distances decreased) at higher dextran concentrations. In contrast, the two S16Thermo mutants did not show any changes in Trp-BODIPY distances upon increase of dextran 20 concentrations. It should be noted that the fluorescence quantum yields and lifetimes of BODIPY attached to the two S16 homologs decreased gradually in the presence of dextran 20. To investigate the origin of this decrease, we studied the BODIPY quantum yield in three protein variants in the presence of a tyrosine-labeled dextran. The experiments revealed distinct tyrosine quenching behaviors of BODIPY in the three variants, suggesting a dynamic local interaction between dextran and one particular S16 variant.
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Affiliation(s)
| | - Jörgen Ådén
- Department of Chemistry, Umeå University, Umeå, Sweden
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21
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Abstract
I spent my childhood and adolescence in North and South Carolina, attended Duke University, and then entered Duke Medical School. One year in the laboratory of George Schwert in the biochemistry department kindled my interest in biochemistry. After one year of residency on the medical service of Duke Hospital, chaired by Eugene Stead, I joined the group of Arthur Kornberg at Stanford Medical School as a postdoctoral fellow. Two years later I accepted a faculty position at Harvard Medical School, where I remain today. During these 50 years, together with an outstanding group of students, postdoctoral fellows, and collaborators, I have pursued studies on DNA replication. I have experienced the excitement of discovering a number of important enzymes in DNA replication that, in turn, triggered an interest in the dynamics of a replisome. My associations with industry have been stimulating and fostered new friendships. I could not have chosen a better career.
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Affiliation(s)
- Charles C Richardson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115;
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22
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Liu Y, Zhu L, Yang J, Sun J, Zhao J, Liang D. Axial growth and fusion of liposome regulated by macromolecular crowding and confinement. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:4822-4826. [PMID: 25874379 DOI: 10.1021/la504699y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The endomembrane system, including the endoplasmic reticulum, Golgi apparatus, lysosomes, and endosomes, is located in the crowded intracellular environment. An understanding of the cellular structure and functions requires knowledge of how macromolecular crowding and confinement affect the activity of membrane and its proteins. Using negatively charged liposome and the peptide K3L8K3 as a model system, we studied the aggregation behavior of liposome in a matrix of polyacrylamide and hyaluronic acid. Without matrix, the liposomes form spherical aggregates in the presence of K3L8K3. However, they orient in one dimension and fuse into a tube up to 40 μm long in the matrix. The growth of the tube is via end-to-end connection. This anisotropic growth is mainly due to the macromolecular confinement provided by the polymer network. The study of the interactions between liposome and peptide in the crowded environment helps to reveal the mechanism of membrane-related processes in vivo.
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Affiliation(s)
- Yun Liu
- †Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Lin Zhu
- †Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Jingfa Yang
- ‡Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Jianbo Sun
- †Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Jiang Zhao
- ‡Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Dehai Liang
- †Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
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23
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Chaudhuri BN. Emerging applications of small angle solution scattering in structural biology. Protein Sci 2015; 24:267-76. [PMID: 25516491 PMCID: PMC4353354 DOI: 10.1002/pro.2624] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 12/05/2014] [Indexed: 12/12/2022]
Abstract
Small angle solution X-ray and neutron scattering recently resurfaced as powerful tools to address an array of biological problems including folding, intrinsic disorder, conformational transitions, macromolecular crowding, and self or hetero-assembling of biomacromolecules. In addition, small angle solution scattering complements crystallography, nuclear magnetic resonance spectroscopy, and other structural methods to aid in the structure determinations of multidomain or multicomponent proteins or nucleoprotein assemblies. Neutron scattering with hydrogen/deuterium contrast variation, or X-ray scattering with sucrose contrast variation to a certain extent, is a convenient tool for characterizing the organizations of two-component systems such as a nucleoprotein or a lipid-protein assembly. Time-resolved small and wide-angle solution scattering to study biological processes in real time, and the use of localized heavy-atom labeling and anomalous solution scattering for applications as FRET-like molecular rulers, are amongst promising newer developments. Despite the challenges in data analysis and interpretation, these X-ray/neutron solution scattering based approaches hold great promise for understanding a wide variety of complex processes prevalent in the biological milieu.
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Affiliation(s)
- Barnali N Chaudhuri
- Faculty of Life Sciences and Biotechnology, South Asian UniversityAkbar Bhawan, Chanakyapuri, New Delhi, India
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24
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Kuznetsova IM, Zaslavsky BY, Breydo L, Turoverov KK, Uversky VN. Beyond the excluded volume effects: mechanistic complexity of the crowded milieu. Molecules 2015; 20:1377-409. [PMID: 25594347 PMCID: PMC6272634 DOI: 10.3390/molecules20011377] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 01/09/2015] [Indexed: 11/16/2022] Open
Abstract
Macromolecular crowding is known to affect protein folding, binding of small molecules, interaction with nucleic acids, enzymatic activity, protein-protein interactions, and protein aggregation. Although for a long time it was believed that the major mechanism of the action of crowded environments on structure, folding, thermodynamics, and function of a protein can be described in terms of the excluded volume effects, it is getting clear now that other factors originating from the presence of high concentrations of “inert” macromolecules in crowded solution should definitely be taken into account to draw a more complete picture of a protein in a crowded milieu. This review shows that in addition to the excluded volume effects important players of the crowded environments are viscosity, perturbed diffusion, direct physical interactions between the crowding agents and proteins, soft interactions, and, most importantly, the effects of crowders on solvent properties.
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Affiliation(s)
- Irina M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia; E-Mails: (I.M.K.); (K.K.T.)
- St. Petersburg State Polytechnical University, 29 Polytechnicheskaya st., St. Petersburg 195251, Russia
| | - Boris Y. Zaslavsky
- Cleveland Diagnostics, 3615 Superior Ave., Suite 4407B, Cleveland, OH 44114, USA; E-Mail:
| | - Leonid Breydo
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33612, USA; E-Mails:
| | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia; E-Mails: (I.M.K.); (K.K.T.)
- St. Petersburg State Polytechnical University, 29 Polytechnicheskaya st., St. Petersburg 195251, Russia
| | - Vladimir N. Uversky
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia; E-Mails: (I.M.K.); (K.K.T.)
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33612, USA; E-Mails:
- Biology Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-813-974-5816; Fax: +1-813-974-7357
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25
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Poggi CG, Slade KM. Macromolecular Crowding and the Steady-State Kinetics of Malate Dehydrogenase. Biochemistry 2014; 54:260-7. [DOI: 10.1021/bi5011255] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher G. Poggi
- Department
of Chemistry, Hobart and William Smith College, Geneva, New York 14456, United States
| | - Kristin M. Slade
- Department
of Chemistry, Hobart and William Smith College, Geneva, New York 14456, United States
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26
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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: 370] [Impact Index Per Article: 37.0] [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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27
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Akabayov SR, Akabayov B, Wagner G. Human translation initiation factor eIF4G1 possesses a low-affinity ATP binding site facing the ATP-binding cleft of eIF4A in the eIF4G/eIF4A complex. Biochemistry 2014; 53:6422-5. [PMID: 25255371 PMCID: PMC4204880 DOI: 10.1021/bi500600m] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Eukaryotic
translation initiation factor 4G (eIF4G) plays a crucial
role in translation initiation, serving as a scaffolding protein binding
several other initiation factors, other proteins, and RNA. Binding
of eIF4G to the ATP-dependent RNA helicase eukaryotic translation
initiation factor 4A (eIF4A) enhances the activity of eIF4A in solution
and in crowded environments. Previously, this activity enhancement
was solely attributed to eIF4G, conferring a closed, active conformation
upon eIF4A. Here we show that eIF4G contains a low-affinity binding
site at the entrance to the ATP-binding cleft on eIF4A, suggesting
that regulation of the local ATP concentration may be an additional
reason for the enhancement in activity.
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Affiliation(s)
- Sabine R Akabayov
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Longwood Avenue, Boston, Massachusetts 02115, United States
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28
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Pitulice L, Vilaseca E, Pastor I, Madurga S, Garcés JL, Isvoran A, Mas F. Monte Carlo simulations of enzymatic reactions in crowded media. Effect of the enzyme-obstacle relative size. Math Biosci 2014; 251:72-82. [DOI: 10.1016/j.mbs.2014.03.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Revised: 02/23/2014] [Accepted: 03/18/2014] [Indexed: 01/21/2023]
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29
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Balcells C, Pastor I, Vilaseca E, Madurga S, Cascante M, Mas F. Macromolecular crowding effect upon in vitro enzyme kinetics: mixed activation-diffusion control of the oxidation of NADH by pyruvate catalyzed by lactate dehydrogenase. J Phys Chem B 2014; 118:4062-8. [PMID: 24660904 DOI: 10.1021/jp4118858] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Enzyme kinetics studies have been usually designed as dilute solution experiments, which differ substantially from in vivo conditions. However, cell cytosol is crowded with a high concentration of molecules having different shapes and sizes. The consequences of such crowding in enzymatic reactions remain unclear. The aim of the present study is to understand the effect of macromolecular crowding produced by dextran of different sizes and at diverse concentrations in the well-known reaction of oxidation of NADH by pyruvate catalyzed by L-lactate dehydrogenase (LDH). Our results indicate that the reaction rate is determined by both the occupied volume and the relative size of dextran obstacles with respect to the enzyme present in the reaction. Moreover, we analyzed the influence of macromolecular crowding on the Michaelis-Menten constants, vmax and Km. The obtained results show that only high concentrations and large sizes of dextran reduce both constants suggesting a mixed activation-diffusion control of this enzymatic reaction due to the dextran crowding action. From our knowledge, this is the first experimental study that depicts mixed activation-diffusion control in an enzymatic reaction due to the effect of crowding.
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Affiliation(s)
- Cristina Balcells
- Department of Physical Chemistry and Research Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona (UB) , 08028 Barcelona, Spain
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30
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Pastor I, Pitulice L, Balcells C, Vilaseca E, Madurga S, Isvoran A, Cascante M, Mas F. Effect of crowding by Dextrans in enzymatic reactions. Biophys Chem 2014; 185:8-13. [DOI: 10.1016/j.bpc.2013.10.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 10/23/2013] [Accepted: 10/26/2013] [Indexed: 11/29/2022]
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31
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Wu HY, Li HW. Crowding alters the dynamics and the length of RecA nucleoprotein filaments in RecA-mediated strand exchange. Chemphyschem 2013; 15:80-4. [PMID: 24281991 DOI: 10.1002/cphc.201300835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 10/24/2013] [Indexed: 11/10/2022]
Abstract
Crowd impact: Molecular crowding effects of bovine serum albumin and poly(ethylene glycol) on the Escherichia coli RecA-mediated strand exchange reaction are quantified by using a single-molecule outgoing strand experiment and magnetic pull-down and ATPase assays. The alterations of the biochemical parameters of this complex enzymatic reaction in such crowded environments are discussed.
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Affiliation(s)
- Hung-Yi Wu
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan (R.O.C). Fax: (+886) 2-2363-6359
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