1
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Alam P, Clovis NS, Chand AK, Khan MF, Sen S. Effect of molecular crowders on ligand binding kinetics with G-quadruplex DNA probed by fluorescence correlation spectroscopy. Methods Appl Fluoresc 2024; 12:045002. [PMID: 39013401 DOI: 10.1088/2050-6120/ad63f5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/16/2024] [Indexed: 07/18/2024]
Abstract
Guanine-rich single-stranded DNA folds into G-quadruplex DNA (GqDNA) structures, which play crucial roles in various biological processes. These structures are also promising targets for ligands, potentially inducing antitumor effects. While thermodynamic parameters of ligand/DNA interactions are well-studied, the kinetics of ligand interaction with GqDNA, particularly in cell-like crowded environments, remain less explored. In this study, we investigate the impact of molecular crowding agents (glucose, sucrose, and ficoll 70) at physiologically relevant concentrations (20% w/v) on the association and dissociation rates of the benzophenoxazine-core based ligand, cresyl violet (CV), with human telomeric antiparallel-GqDNA. We utilized fluorescence correlation spectroscopy (FCS) along with other techniques. Our findings reveal that crowding agents decrease the binding affinity of CV to GqDNA, with the most significant effect-a nearly three-fold decrease-observed with ficoll 70. FCS measurements indicate that this decrease is primarily due to a viscosity-induced slowdown of ligand association in the crowded environment. Interestingly, dissociation rates remain largely unaffected by smaller crowders, with only small effect observed in presence of ficoll 70 due to direct but weak interaction between the ligand and ficoll. These results along with previously reported data provide valuable insights into ligand/GqDNA interactions in cellular contexts, suggesting a conserved mechanism of saccharide crowder influence, regardless of variations in GqDNA structure and ligand binding mode. This underscores the importance of considering crowding effects in the design and development of GqDNA-targeted drugs for potential cancer treatment.
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Affiliation(s)
- Parvez Alam
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ndege Simisi Clovis
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ajay Kumar Chand
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Mohammad Firoz Khan
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sobhan Sen
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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2
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Ghosh S, Prabhu NP. Heterogeneous Macromolecular crowding effect on nucleation-independent fibril formation of Lysozyme: Spectroscopic analysis of Structure, Stability, and fibrillation rate. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 315:124276. [PMID: 38626673 DOI: 10.1016/j.saa.2024.124276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 04/18/2024]
Affiliation(s)
- Subhasree Ghosh
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - N Prakash Prabhu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
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3
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Grassmann G, Miotto M, Desantis F, Di Rienzo L, Tartaglia GG, Pastore A, Ruocco G, Monti M, Milanetti E. Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments. Chem Rev 2024; 124:3932-3977. [PMID: 38535831 PMCID: PMC11009965 DOI: 10.1021/acs.chemrev.3c00550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 04/11/2024]
Abstract
Investigating protein-protein interactions is crucial for understanding cellular biological processes because proteins often function within molecular complexes rather than in isolation. While experimental and computational methods have provided valuable insights into these interactions, they often overlook a critical factor: the crowded cellular environment. This environment significantly impacts protein behavior, including structural stability, diffusion, and ultimately the nature of binding. In this review, we discuss theoretical and computational approaches that allow the modeling of biological systems to guide and complement experiments and can thus significantly advance the investigation, and possibly the predictions, of protein-protein interactions in the crowded environment of cell cytoplasm. We explore topics such as statistical mechanics for lattice simulations, hydrodynamic interactions, diffusion processes in high-viscosity environments, and several methods based on molecular dynamics simulations. By synergistically leveraging methods from biophysics and computational biology, we review the state of the art of computational methods to study the impact of molecular crowding on protein-protein interactions and discuss its potential revolutionizing effects on the characterization of the human interactome.
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Affiliation(s)
- Greta Grassmann
- Department
of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, Rome 00185, Italy
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
| | - Mattia Miotto
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
| | - Fausta Desantis
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- The
Open University Affiliated Research Centre at Istituto Italiano di
Tecnologia, Genoa 16163, Italy
| | - Lorenzo Di Rienzo
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
| | - Gian Gaetano Tartaglia
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- Department
of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genoa 16163, Italy
- Center
for Human Technologies, Genoa 16152, Italy
| | - Annalisa Pastore
- Experiment
Division, European Synchrotron Radiation
Facility, Grenoble 38043, France
| | - Giancarlo Ruocco
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- Department
of Physics, Sapienza University, Rome 00185, Italy
| | - Michele Monti
- RNA
System Biology Lab, Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genoa 16163, Italy
| | - Edoardo Milanetti
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- Department
of Physics, Sapienza University, Rome 00185, Italy
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4
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Majumdar S, Rastogi H, Chowdhury PK. Bridging Soft Interaction and Excluded Volume in Crowded Milieu through Subtle Protein Dynamics. J Phys Chem B 2024; 128:716-730. [PMID: 38226816 DOI: 10.1021/acs.jpcb.3c07266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
The impact of macromolecular crowding on biological macromolecules has been elucidated through the excluded volume phenomenon and soft interactions. However, it has often been difficult to provide a clear demarcation between the two regions. Here, using temperature-dependent dynamics (local and global) of the multidomain protein human serum albumin (HSA) in the presence of commonly used synthetic crowders (Dextran 40, PEG 8, Ficoll 70, and Dextran 70), we have shown the presence of a transition that serves as a bridge between the soft and hard regimes. The bridging region is independent of the crowder identity and displays no apparent correlation with the critical overlap concentration of the polymeric crowding agents. Moreover, the dynamics of domains I and II and the protein gating motion respond differently, thereby bringing to the fore the asymmetry underlying the crowder influence on HSA. In addition, solvent-coupled and decoupled protein motions indicate the heterogeneity of the dynamic landscape in the crowded milieu. We also propose an intriguing correlation between protein stability and dynamics, with increased global stability being accompanied by eased local domain motion.
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Affiliation(s)
- Shubhangi Majumdar
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - 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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5
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Seitz C, Deveci İ, McCammon JA. Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics. J Phys Chem Lett 2023; 14:9926-9934. [PMID: 37903229 PMCID: PMC10641874 DOI: 10.1021/acs.jpclett.3c02524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/01/2023]
Abstract
All protein simulations are conducted with varying degrees of simplification, oftentimes with unknown ramifications about how these simplifications affect the interpretability of the results. In this work, we investigated how protein glycosylation and lateral crowding effects modulate an array of properties characterizing the stability and dynamics of influenza neuraminidase. We constructed three systems: (1) glycosylated neuraminidase in a whole virion (i.e., crowded membrane) environment, (2) glycosylated neuraminidase in its own lipid bilayer, and (3) unglycosylated neuraminidase in its own lipid bilayer. We saw that glycans tend to stabilize the protein structure and reduce its conformational flexibility while restricting the solvent movement. Conversely, a crowded membrane environment encouraged exploration of the free energy landscape and a large-scale conformational change, while making the protein structure more compact. Understanding these effects informs what factors one must consider in attempting to recapture the desired level of physical accuracy.
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Affiliation(s)
- Christian Seitz
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - İlker Deveci
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - J. Andrew McCammon
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
- Department
of Pharmacology, University of California,
San Diego, La Jolla, California 92093, United States
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6
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Olgenblum GI, Carmon N, Harries D. Not Always Sticky: Specificity of Protein Stabilization by Sugars Is Conferred by Protein-Water Hydrogen Bonds. J Am Chem Soc 2023; 145:23308-23320. [PMID: 37845197 PMCID: PMC10603812 DOI: 10.1021/jacs.3c08702] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Solutes added to buffered solutions directly impact protein folding. Protein stabilization by cosolutes or crowders has been shown to be largely driven by protein-cosolute volume exclusion complemented by chemical and soft interactions. By contrast to previous studies that indicate the invariably destabilizing role of soft protein-sugar attractions, we show here that soft interactions with sugar cosolutes are protein-specific and can be stabilizing or destabilizing. We experimentally follow the folding of two model miniproteins that are only marginally stable but in the presence of sugars and polyols fold into representative and distinct secondary structures: β-hairpin or α-helix. Our mean-field model reveals that while protein-sugar excluded volume interactions have a similar stabilizing effect on both proteins, the soft interactions add a destabilizing contribution to one miniprotein but further stabilize the other. Using molecular dynamics simulations, we link the soft protein-cosolute interactions to the weakening of direct protein-water hydrogen bonding due to the presence of sugars. Although these weakened hydrogen bonds destabilize both the native and denatured states of the two proteins, the resulting contribution to the folding free energy can be positive or negative depending on the amino acid sequence. This study indicates that the significant variation between proteins in their soft interactions with sugar determines the specific response of different proteins, even to the same sugar.
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Affiliation(s)
- Gil I Olgenblum
- The Fritz Haber Research Center, and the Harvey M. Kruger Center for Nanoscience & Nanotechnology, Institute of Chemistry, The Hebrew University, Jerusalem 9190401, Israel
| | - Neta Carmon
- The Fritz Haber Research Center, and the Harvey M. Kruger Center for Nanoscience & Nanotechnology, Institute of Chemistry, The Hebrew University, Jerusalem 9190401, Israel
| | - Daniel Harries
- The Fritz Haber Research Center, and the Harvey M. Kruger Center for Nanoscience & Nanotechnology, Institute of Chemistry, The Hebrew University, Jerusalem 9190401, Israel
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7
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Seitz C, Deveci İ, McCammon JA. Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.10.556910. [PMID: 37745347 PMCID: PMC10515755 DOI: 10.1101/2023.09.10.556910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
All protein simulations are conducted with varying degrees of simplifications, oftentimes with unknown ramifications on how these simplifications affect the interpretability of the results. In this work we investigated how protein glycosylation and lateral crowding effects modulate an array of properties characterizing the stability and dynamics of influenza neuraminidase. We constructed three systems: 1) Glycosylated neuraminidase in a whole virion (i.e. crowded membrane) environment 2) Glycosylated neuraminidase in its own lipid bilayer 3) Unglycosylated neuraminidase in its own lipid bilayer. We saw that glycans tend to stabilize the protein structure and reduce its conformational flexibility while restricting solvent movement. Conversely, a crowded membrane environment encouraged exploration of the free energy landscape and a large scale conformational change while making the protein structure more compact. Understanding these effects informs what factors one must consider while attempting to recapture the desired level of physical accuracy.
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Affiliation(s)
- Christian Seitz
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - İlker Deveci
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
- Department of Pharmacology, University of California, San Diego, La Jolla, California
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8
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Knab E, Davis CM. Chemical interactions modulate λ 6-85 stability in cells. Protein Sci 2023; 32:e4698. [PMID: 37313657 PMCID: PMC10288553 DOI: 10.1002/pro.4698] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/26/2023] [Accepted: 06/06/2023] [Indexed: 06/15/2023]
Abstract
Because steric crowding is most effective when the crowding agent is similar in size to the molecule that it acts upon and the average macromolecule inside cells is much larger than a small protein or peptide, steric crowding is not predicted to affect their folding inside cells. On the other hand, chemical interactions should perturb in-cell structure and stability because they arise from interactions between the surface of the small protein or peptide and its environment. Indeed, previous in vitro measurements of the λ-repressor fragment, λ6-85 , in crowding matrices comprised of Ficoll or protein crowders support these predictions. Here, we directly quantify the in-cell stability of λ6-85 and distinguish the contribution of steric crowding and chemical interactions to its stability. Using a FRET-labeled λ6-85 construct, we find that the fragment is stabilized by 5°C in-cells compared to in vitro. We demonstrate that this stabilization cannot be explained by steric crowding because, as anticipated, Ficoll has no effect on λ6-85 stability. We find that the in-cell stabilization arises from chemical interactions, mimicked in vitro by mammalian protein extraction reagent (M-PER™). Comparison between FRET values in-cell and in Ficoll confirms that U-2 OS cytosolic crowding is reproduced at macromolecule concentrations of 15% w/v. Our measurements validate the cytomimetic of 15% Ficoll and 20% M-PER™ that we previously developed for protein and RNA folding studies. However, because the in-cell stability of λ6-85 is reproduced by 20% v/v M-PER™ alone, we predict that this simplified mixture could be a useful tool to predict the in-cell behaviors of other small proteins and peptides.
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Affiliation(s)
- Edward Knab
- Department of ChemistryYale UniversityNew HavenConnecticutUSA
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9
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Irukuvajjula SS, Jithender Reddy G, Rao K, Vadrevu LR. Contrasting effect of ficoll on apo and holo forms of bacterial chemotaxis protein Y: Selective destabilization of the conformationally altered holo form. Int J Biol Macromol 2023; 232:123505. [PMID: 36736516 DOI: 10.1016/j.ijbiomac.2023.123505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/13/2023] [Accepted: 01/28/2023] [Indexed: 02/04/2023]
Abstract
Chemotaxis Y (CheY), upon metal binding, displays a drastic alteration in its structure and stability. This premise prompted us to study the effect of crowding on the two conformationally distinct states of the same test protein. A comparative analysis on the structure and thermal stability in the presence and absence of the macromolecular crowder, ficoll, and its monomeric unit, sucrose, revealed a contrasting effect of ficoll on the apo and holo forms. In the presence of ficoll while the thermal stability (Tm) of the apo form is enhanced, the thermal stability of the holo form is reduced. The selective lowering of Tm for the holo form in the combined presence of ficoll and sucrose and not in sucrose alone suggests that the contrasting effect is due to the macromolecular nature of ficoll. Since metal-protein interaction remains unperturbed in the presence of ficoll and Mg2+ sequestration is ruled out in a systematic manner the alternative possibility for the exclusive reduction in the thermal stability of the holo form is the ficoll-induced modulation of the relative population of apo and holo forms of CheY.
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Affiliation(s)
- Shivkumar Sharma Irukuvajjula
- Department of Biological Sciences, Birla Institute of Science and Technology - Pilani, Hyderabad Campus, Shamirpet, Hyderabad 500078, India.
| | - G Jithender Reddy
- NMR Division, Department of Analytical & Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Ministry of Science and Technology, Uppal Road, Tarnaka, Hyderabad 500007, India
| | - Krishna Rao
- Tata Institute of Fundamental Research, 36/P, Gopanpally Mandal, Ranga Reddy District, Hyderabad, Telangana State 500107, India
| | - Late Ramakrishna Vadrevu
- Department of Biological Sciences, Birla Institute of Science and Technology - Pilani, Hyderabad Campus, Shamirpet, Hyderabad 500078, India
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10
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Connecting the Dots: Macromolecular Crowding and Protein Aggregation. J Fluoresc 2023; 33:1-11. [PMID: 36417150 DOI: 10.1007/s10895-022-03082-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/09/2022] [Indexed: 11/24/2022]
Abstract
Proteins are one of the dynamic macromolecules that play a significant role in many physiologically important processes to sustain life on the earth. Proteins need to be properly folded into their active conformation to perform their function. Alteration in the protein folding process may lead to the formation of misfolded conformers. Accumulation of these misfolded conformers can result in the formation of protein aggregates which are attributed to many human pathological conditions including neurodegeneration, cataract, neuromuscular disorders, and diabetes. Living cells naturally have heterogeneous crowding environments with different concentrations of various biomolecules. Macromolecular crowding condition has been found to alter the protein conformation. Here in this review, we tried to show the relation between macromolecular crowding, protein aggregation, and its consequences.
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11
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Raina N, Hassan MI, Ahmad F, Islam A, Singh AK. PEG mediated destabilization of holo α-lactalbumin probed by in silico and in vitro studies: deviation from excluded volume effect. J Biomol Struct Dyn 2022; 40:13265-13277. [PMID: 34726117 DOI: 10.1080/07391102.2021.1987990] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Crowded and confined macromolecular milieus surround proteins, and both are stabilizing if the nature of the interaction between crowder and proteins are considered hard-core repulsive interactions. However, non-specific chemical interactions between a protein and its surroundings also play a significant role and the sum effect of both hard-core repulsion and soft interaction balances the overall effect of crowding/confinement. Previous studies showing the effect of polyethylene glycol (PEG) on protein and nucleic acid may be interpreted as either primarily excluded volume effect or, in some cases, chemical effect by changing solvent properties. In case of destabilizing interactions, charge-charge and hydrophobic contact have to gain more attention. For instance, in vitro and in vivo studies using protein as crowding agent revealed the destabilization of proteins induced by charge-charge interactions. To investigate the effect of PEG 10 kDa on holo α-lactalbumin (holo α-LA), structure and thermal stability of the protein were measured at different pH values using several techniques. Structural characterization by Trp-fluorescence, near-UV CD and far-UV measurements at different pH values clearly shows perturbation of tertiary and secondary structure of holo α-LA by PEG 10 kDa. Furthermore, the dynamic light scattering measurement shows that the protein is homogeneous under all experimental conditions. Analysis of the heat-induced denaturation profile in the presence of the crowder shows destabilization of the protein in terms of Tm (midpoint of denaturation) and ΔGD0 (Gibbs free energy change at 25 °C). To evaluate the interaction of PEG 10 kDa with holo α-LA and stability of PEG-α-LA complex, docking and molecular dynamic simulation were carried out for 100 ns.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neha Raina
- Department of Biotechnology, Sharda University, Greater Noida, Uttar Pradesh, India.,Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, Delhi, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, Delhi, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, Delhi, India
| | - Amit Kumar Singh
- Department of Biotechnology, Sharda University, Greater Noida, Uttar Pradesh, India
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12
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Simisi Clovis N, Alam P, Kumar Chand A, Sardana D, Firoz Khan M, Sen S. Molecular Crowders Modulate Ligand Binding Affinity to G-Quadruplex DNA by Decelerating Ligand Association. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2022.114432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Mondal S, Das S, Swamy MJ. Macromolecular Crowding Significantly Affects the Conformational Features and Carbohydrate Binding Properties of CIA17, a PP2-Type Lectin from Coccinia indica. Biochemistry 2022; 61:2344-2357. [PMID: 36200563 DOI: 10.1021/acs.biochem.2c00389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effect of macromolecular crowding on the conformational features and carbohydrate binding properties of CIA17, a PP2-type lectin, was investigated employing polymeric dextrans D6, D40, and D70 (Mr ∼ 6, 40, and 70 kDa, respectively) as crowders. While the secondary structure of CIA17 was significantly affected by D6, with a considerable decrease in the number of β-sheets and β-turns with a corresponding increase in the number of unordered structures, relatively smaller changes were induced by D40 and D70. However, differential scanning calorimetry (DSC) studies revealed that the thermal stability of the protein remains unchanged in the presence of crowders. While the larger dextrans, D70 and D40, induced modest quenching (∼10%) of the protein fluorescence by a static pathway, the smaller D6 induced a higher degree of quenching (37%), which involved both static and collisional quenching processes. The results of fluorescence correlation spectroscopy measurements together with DSC studies suggested that CIA17 forms larger oligomers in the presence of D40 and D70 but D6 prevents the formation of higher-order oligomers. The association constant for the CIA17-chitooligosaccharide interaction increased by ∼30% and 160% in the presence of D40 and D70, respectively, but decreased by ∼30% in the presence of D6. The higher binding affinity can be attributed to the excluded volume effect, i.e., an increased effective concentration of the protein in the presence of D40 and D70, whereas D6, being smaller, possibly penetrates into the protein interior, disrupting the water structure around the protein and also inducing conformational changes, resulting in weaker binding. These observations demonstrate that molecular crowding significantly affects the carbohydrate binding characteristics of lectins, which can modulate their physiological function.
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Affiliation(s)
- Saradamoni Mondal
- School of Chemistry, University of Hyderabad, Hyderabad500 046, India
| | - Somnath Das
- School of Chemistry, University of Hyderabad, Hyderabad500 046, India
| | - Musti J Swamy
- School of Chemistry, University of Hyderabad, Hyderabad500 046, India
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14
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Raina N, Khan S, Soundhararajan R, Shahid M, Srinivasan H, Islam A. Understanding the nano colloid-protein interaction in crowded milieu. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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15
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Pal S, Mitra RK. Nonpolar hydrophobic amino acids tune the enzymatic activity of lysozyme. Biophys Chem 2022; 288:106842. [PMID: 35696897 DOI: 10.1016/j.bpc.2022.106842] [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: 02/15/2022] [Revised: 05/19/2022] [Accepted: 05/26/2022] [Indexed: 11/02/2022]
Abstract
We have used five different hydrophobic L-amino acids (Gly, Ala, Val, Leu, Ile) as molecular crowders to investigate their role on the enzymatic activity of lysozyme towards Micrococcus lysodeikticus (M. lys.)cell as substrate. We found that except Ile, all other amino acids show a bell like profile of catalytic efficiency (kcat/Km) with their increasing concentration whereas for Ile, the value is gradually increasing. The trend of activation energy (Ea) is also well correlated with the catalytic efficiency of lysozyme. At low concentration of amino acids, soft interaction predominates whereas at higher concentration range, excluded volume, viscosity, hydrophobicity combinedly decrease the activity of lysozyme.
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Affiliation(s)
- Saikat Pal
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India
| | - Rajib Kumar Mitra
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India.
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16
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Mondarte EAQ, Zamarripa EMM, Chang R, Wang F, Song S, Tahara H, Hayashi T. Interphase Protein Layers Formed on Self-Assembled Monolayers in Crowded Biological Environments: Analysis by Surface Force and Quartz Crystal Microbalance Measurements. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:1324-1333. [PMID: 35029393 DOI: 10.1021/acs.langmuir.1c02312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We investigated a viscous protein layer formed on self-assembled monolayers (SAMs) in crowded biological environments. The results were obtained through force spectroscopic measurements using colloidal probes and substantiated by exhaustive analysis using a quartz crystal microbalance with an energy dissipation technique. A hydrophobic SAM of n-octanethiol (C8 SAM) in bovine serum albumin (BSA) solution is buried under an adlayer of denatured BSA molecules and an additional viscous interphase layer that is five times more viscous than the bulk solution. C8 SAMs in fetal bovine serum induced a formation of a thicker adsorbed protein layer but with no observable viscous interphase layer. These findings show that a fouling surface is essentially inaccessible to any approaching molecules and thus has a new biological and physical identity arising from its surrounding protein layers. In contrast, the SAMs composed of sulfobetaine-terminated alkanethiol proved to be sufficiently protein-resistant and bio-inert even under crowded conditions due to a protective barrier of its interfacial water, which has implications in the accurate targeting of artificial particles for drug delivery and similar applications by screening any non-specific interactions. Finally, our strategies provide a platform for the straightforward yet effectual in vitro characterization of diverse types of surfaces in the context of targeted interactions in crowded biological environments.
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Affiliation(s)
- Evan Angelo Quimada Mondarte
- Tokyo Institute of Technology, Department of Materials Science and Engineering, School of Materials and Chemical Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
| | - Elisa Margarita Mendoza Zamarripa
- Tokyo Institute of Technology, Department of Materials Science and Engineering, School of Materials and Chemical Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
| | - Ryongsok Chang
- Tokyo Institute of Technology, Department of Materials Science and Engineering, School of Materials and Chemical Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
| | - Fan Wang
- Tokyo Institute of Technology, Department of Materials Science and Engineering, School of Materials and Chemical Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
| | - Subin Song
- Tokyo Institute of Technology, Department of Materials Science and Engineering, School of Materials and Chemical Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
| | - Hiroyuki Tahara
- Tokyo Institute of Technology, Department of Materials Science and Engineering, School of Materials and Chemical Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
| | - Tomohiro Hayashi
- Tokyo Institute of Technology, Department of Materials Science and Engineering, School of Materials and Chemical Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
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17
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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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18
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Das N, Sen P. Macromolecular Crowding Effect on the Structure, Function, Conformational Dynamics and Relative Domain Movement of a Multi-Domain Protein as a function of Crowder Shape and Interaction. Phys Chem Chem Phys 2022; 24:14242-14256. [DOI: 10.1039/d1cp04842b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The cellular environment is crowded by macromolecules of various sizes, shapes, and charges, which modulate protein structure, function and dynamics. Herein, we contemplated the effect of three different macromolecular crowders:...
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19
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Contessoto VG, Ferreira PHB, Chahine J, Leite VBP, Oliveira RJ. Small Neutral Crowding Solute Effects on Protein Folding Thermodynamic Stability and Kinetics. J Phys Chem B 2021; 125:11673-11686. [PMID: 34644091 DOI: 10.1021/acs.jpcb.1c07663] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular crowding is a ubiquitous phenomenon in biological systems, with significant consequences on protein folding and stability. Small compounds, such as the osmolyte trimethylamine N-oxide (TMAO), can also present similar effects. To analyze the effects arising from these solute-like molecules, we performed a series of crowded coarse-grained folding simulations. Two well-known proteins were chosen, CI2 and SH3, modeled by the alpha-carbon-structure-based model. In the simulations, the crowding molecules were represented by low-sized neutral atom beads in different concentrations. The results show that a low level of the volume fraction occupied by neutral agents can change protein stability and folding kinetics for the two systems. However, the kinetics were shown to be unaffected in their respective folding temperatures. The faster kinetics correlates with changes in the folding route for systems at the same temperature, where non-native contacts were shown to be relevant. The transition states of the two systems with and without crowders are similar. In the case of SH3, there are differences in the structuring of two strands, which may be associated with the increase in its folding rate, in addition to the destabilization of the denatured ensemble. The present study also detected a crossover in the thermodynamic stability behavior, previously observed experimentally and theoretically. As the temperature increases, crowders change from destabilizing to stabilizing agents.
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Affiliation(s)
- Vinícius G Contessoto
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences, São Paulo State University, São José do Rio Preto 15054-000, Brazil
| | - Paulo H B Ferreira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba 38064-200, Brazil
| | - Jorge Chahine
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences, São Paulo State University, São José do Rio Preto 15054-000, Brazil
| | - Vitor B P Leite
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences, São Paulo State University, São José do Rio Preto 15054-000, Brazil
| | - Ronaldo J Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba 38064-200, Brazil
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20
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Kim R, Radhakrishnan ML. Macromolecular crowding effects on electrostatic binding affinity: Fundamental insights from theoretical, idealized models. J Chem Phys 2021; 154:225101. [PMID: 34241219 DOI: 10.1063/5.0042082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The crowded cellular environment can affect biomolecular binding energetics, with specific effects depending on the properties of the binding partners and the local environment. Often, crowding effects on binding are studied on particular complexes, which provide system-specific insights but may not provide comprehensive trends or a generalized framework to better understand how crowding affects energetics involved in molecular recognition. Here, we use theoretical, idealized molecules whose physical properties can be systematically varied along with samplings of crowder placements to understand how electrostatic binding energetics are altered through crowding and how these effects depend on the charge distribution, shape, and size of the binding partners or crowders. We focus on electrostatic binding energetics using a continuum electrostatic framework to understand effects due to depletion of a polar, aqueous solvent in a crowded environment. We find that crowding effects can depend predictably on a system's charge distribution, with coupling between the crowder size and the geometry of the partners' binding interface in determining crowder effects. We also explore the effect of crowder charge on binding interactions as a function of the monopoles of the system components. Finally, we find that modeling crowding via a lowered solvent dielectric constant cannot account for certain electrostatic crowding effects due to the finite size, shape, or placement of system components. This study, which comprehensively examines solvent depletion effects due to crowding, complements work focusing on other crowding aspects to help build a holistic understanding of environmental impacts on molecular recognition.
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Affiliation(s)
- Rachel Kim
- Department of Chemistry, Wellesley College, Wellesley, Massachusetts 02481, USA
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21
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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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22
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Tang S, Wang W, Zhang X. Direct visualization and profiling of protein misfolding and aggregation in live cells. Curr Opin Chem Biol 2021; 64:116-123. [PMID: 34246835 DOI: 10.1016/j.cbpa.2021.05.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/27/2021] [Accepted: 05/09/2021] [Indexed: 10/20/2022]
Abstract
Over the past few years, research tools have been developed to monitor the multistep protein aggregation process in live cells, a process that has been associated with a growing number of human diseases. Herein, we describe recent advances in methods that can either survey the distribution of aggregation at the level of the cellular proteome using mass spectroscopy or discern the multistep aggregation process of specific proteins of interest via fluorescence signals. Future development and application of such technologies are expected to provide insights on mechanisms, diagnosis, and treatment of diseases rooted in protein aggregation.
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Affiliation(s)
- Sicheng Tang
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, United States.
| | - Wenting Wang
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, United States
| | - Xin Zhang
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, United States; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, United States.
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23
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Kumar S, Gallagher R, Bishop J, Kline E, Buser J, Lafleur L, Shah K, Lutz B, Yager P. Long-term dry storage of enzyme-based reagents for isothermal nucleic acid amplification in a porous matrix for use in point-of-care diagnostic devices. Analyst 2021; 145:6875-6886. [PMID: 32820749 DOI: 10.1039/d0an01098g] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nucleic acid amplification test (NAAT)-based point-of-care (POC) devices are rapidly growing for use in low-resource settings. However, key challenges are the ability to store the enzyme-based reagents in dry form in the device and the long-term stability of those reagents at elevated temperatures, especially where ambient temperatures could be as high as 45 °C. Here, we describe a set of excipients including a combination of trehalose, polyethylene glycol and dextran, and a method for using them that allows long-term dry storage of enzyme-based reagents for an isothermal strand displacement amplification (iSDA) reaction in a porous matrix. Various porous materials, including nitrocellulose, cellulose, and glass fiber, were tested. Co-dried reagents for iSDA always included those that amplified the ldh1 gene in Staphylococcus aureus (a polymerase and a nicking enzyme, 4 primers, dNTPs and a buffer). Reagents also either included a capture probe and a streptavidin-Au label required for lateral flow (LF) detection after amplification, or a fluorescent probe used for real-time detection. The reagents showed the best stability in a glass fiber matrix when stored in the presence of 10% trehalose and 2.5% dextran. The reagents were stable for over a year at ∼22 °C as determined by lateral flow detection and gel electrophoresis. The reagents also exhibited excellent stability after 360 h at 45 °C; the assay still detected as few as 10 copies of ldh1 gene target by lateral flow detection, and 50 copies with real-time fluorescence detection. These results demonstrate the potential for incorporation of amplification reagents in dry form in point-of-care devices for use in a wide range of settings.
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Affiliation(s)
- Sujatha Kumar
- Department of Bioengineering, University of Washington, 3720 15th Ave NE, Seattle, Washington, USA.
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24
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Abstract
Bioelectrocatalysis using redox enzymes appears as a sustainable way for biosensing, electricity production, or biosynthesis of fine products. Despite advances in the knowledge of parameters that drive the efficiency of enzymatic electrocatalysis, the weak stability of bioelectrodes prevents large scale development of bioelectrocatalysis. In this review, starting from the understanding of the parameters that drive protein instability, we will discuss the main strategies available to improve all enzyme stability, including use of chemicals, protein engineering and immobilization. Considering in a second step the additional requirements for use of redox enzymes, we will evaluate how far these general strategies can be applied to bioelectrocatalysis.
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25
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Nasreen K, Parray ZA, Shamsi A, Ahmad F, Ahmed A, Malik A, Lakhrm NA, Hassan MI, Islam A. Crowding Milleu stabilizes apo-myoglobin against chemical-induced denaturation: Dominance of hardcore repulsions in the heme devoid protein. Int J Biol Macromol 2021; 181:552-560. [PMID: 33744250 DOI: 10.1016/j.ijbiomac.2021.03.089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 12/27/2022]
Abstract
Macromolecular crowding can have significant consequences on the structure and dynamics of a protein. The size and shape of a co-solute molecule and the nature of protein contribute significantly in macromolecular crowding, which results in different outcomes in similar conditions. The structure of apo-myoglobin (apo-Mb) both in the absence and presence of denaturants (GdmCl and urea) was investigated in crowded conditions at pH 7.0, with a comparable size of crowders (~70 kDa) but of different shapes (ficoll and dextran) at various concentrations using spectroscopic techniques like absorption and circular dichroism to monitor changes in secondary and tertiary structure, respectively. The crowders in the absence of denaturants showed structural stabilization of the tertiary structure while no significant change in the secondary structure was observed. The effect of crowders on the stability of the protein was also investigated using probes such as Δε291 and θ222 using chemical denaturants. The analysis of chemical-induced denaturation curves showed that both the crowders stabilize apo-Mb by increasing the values of the midpoint of transition (Cm) and change in free energy in the absence of denaturant (∆GD°), and it was observed that dextran 70 shows more stabilization than ficoll 70 under similar conditions. In this study apo-Mb showed stabilization under crowded conditions, which is a deviation from earlier work from our group where holo form of the same protein was destabilized. This study emphasizes that volume exclusion is a dominant force in a simple protein while soft interactions may play important role in the proteins that are possessing prosthetic group. Hence, the effect of crowders is protein-dependent, and excluded volume plays a great role in the stabilization of apo-Mb, which does not interact with the crowders.
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Affiliation(s)
- Khalida Nasreen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Zahoor Ahmad Parray
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Anwar Ahmed
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ajamaluddin Malik
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Nasser Abobakr Lakhrm
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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26
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Response to crowded conditions reveals compact nucleus for amyloid formation of folded protein. QRB DISCOVERY 2021. [PMID: 37529678 PMCID: PMC10392690 DOI: 10.1017/qrd.2020.17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Abstract
Although the consequences of the crowded cell environments may affect protein folding, function and misfolding reactions, these processes are often studied in dilute solutions in vitro. We here used biophysical experiments to investigate the amyloid fibril formation process of the fish protein apo-β-parvalbumin in solvent conditions that mimic steric and solvation aspects of the in vivo milieu. Apo-β-parvalbumin is a folded protein that readily adopts an amyloid state via a nucleation–elongation mechanism. Aggregation experiments in the presence of macromolecular crowding agents (probing excluded volume, entropic effects) as well as small molecule osmolytes (probing solvation, enthalpic effects) revealed that both types of agents accelerate overall amyloid formation, but the elongation step was faster with macromolecular crowding agents but slower in the presence of osmolytes. The observations can be explained by the steric effects of excluded volume favoring assembled states and that amyloid nucleation does not involve monomer unfolding. In contrast, the solvation effects due to osmolyte presence promote nucleation but not elongation. Therefore, the amyloid-competent nuclei must be compact with less osmolytes excluded from the surface than either the folded monomers or amyloid fibers. We conclude that, in contrast to other amyloidogenic folded proteins, amyloid formation of apo-β-parvalbumin is accelerated by crowded cell-like conditions due to a nucleation process that does not involve large-scale protein unfolding.
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27
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Cozzolino S, Graziano G. The magnitude of macromolecular crowding caused by Dextran and Ficoll for the conformational stability of globular proteins. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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28
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Taylor MP, Vinci C, Suzuki R. Effects of macromolecular crowding on the folding of a polymer chain: A Wang-Landau simulation study. J Chem Phys 2020; 153:174901. [PMID: 33167653 DOI: 10.1063/5.0025640] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A flexible polymer chain in the presence of inert macromolecular crowders will experience a loss of configurational entropy due to the crowder excluded volume. This entropy reduction will be most pronounced in good solvent conditions where the chain assumes an expanded coil conformation. For polymers that undergo a folding transition from a coil to a compact ordered state, as is the case for many globular proteins, macromolecular crowding is expected to stabilize the folded state and thereby shift the transition location. Here, we study such entropic stabilization effects for a tangent square-well sphere chain (monomer diameter σ) in the presence of hard-sphere (HS) crowders (diameter D ≥ σ). We use the Wang-Landau simulation algorithm to construct the density of states for this chain in a crowded environment and are thus able to directly compute the reduction in configurational entropy due to crowding. We study both a chain that undergoes all-or-none folding directly from the coil state and a chain that folds via a collapsed-globule intermediate state. In each case, we find an increase in entropic stabilization for the compact states with an increase in crowder density and, for fixed crowder density, with a decrease in crowder size (concentrated, small crowders have the largest effect). The crowder significantly reduces the average size for the unfolded states while having a minimal effect on the size of the folded states. In the athermal limit, our results directly provide the confinement free energy due to crowding for a HS chain in a HS solvent.
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Affiliation(s)
- Mark P Taylor
- Department of Physics, Hiram College, Hiram, Ohio 44234, USA
| | | | - Ryogo Suzuki
- Department of Physics, Hiram College, Hiram, Ohio 44234, USA
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29
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Consequence of macromolecular crowding on aggregation propensity and structural stability of haemoglobin under glycating conditions. Int J Biol Macromol 2020; 162:1044-1053. [PMID: 32553973 DOI: 10.1016/j.ijbiomac.2020.06.127] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/31/2020] [Accepted: 06/12/2020] [Indexed: 12/20/2022]
Abstract
Cell interiors are extremely congested with biological macromolecules exerting crowding effect, influencing various physiognomies of protein life. Present work deals with effect of crowding on folding behaviour of haemoglobin (Hb) under glycating conditions. Macromolecular crowding was mimicked by concentrated solutions of dextran 70. Hb with 0.2 M fructose and ribose was incubated separately for 96 h in dilute and crowded solution to analyse conformational changes. Reduced intrinsic and ANS fluorescence, decreased Soret absorbance, enhanced turbidity, browning of protein, red shift in ThT and Congo red spectra significantly unveiled protein aggregation. FTIR and CD results revealed transition from α-helix to β-sheets confirming aggregation. Transmission electron microscopy exhibited incidence of aggregates. Macromolecular crowding was witnessed to defend conformational stability of native Hb under stress condition at 100 mg/ml dextran, noticeably indicating deceleration of aggregation. Stabilising effect of crowding was marginally better in fructosylated Hb than with ribose due to difference in their glycation potential. Contrarily, in over-crowded solution where dextran concentration was 500 mg/ml, heightened aggregation was perceived implying concentration dependant, dual nature of macromolecular crowding. The novelty of this study lies in idea of considering macromolecular crowding as a key player in regulation of protein stability which was safely ignored previously.
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30
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Das N, Sen P. Shape-Dependent Macromolecular Crowding on the Thermodynamics and Microsecond Conformational Dynamics of Protein Unfolding Revealed at the Single-Molecule Level. J Phys Chem B 2020; 124:5858-5871. [DOI: 10.1021/acs.jpcb.0c03897] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Nilimesh Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP India
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP India
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31
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Conformational Dynamics from Ambiguous Zinc Coordination in the RanBP2-Type Zinc Finger of RBM5. J Mol Biol 2020; 432:4127-4138. [PMID: 32450081 DOI: 10.1016/j.jmb.2020.05.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 11/22/2022]
Abstract
The multi-domain RNA binding protein RBM5 is a molecular signature of metastasis. RBM5 regulates alternative splicing of apoptotic genes including the cell death receptor Fas and the initiator Caspase-2. The RBM5 RanBP2-type zinc finger (Zf1) is known to specifically recognize single-stranded RNAs with high affinity. Here, we study the structure and conformational dynamics of the Zf1 zinc finger of human RBM5 using NMR. We show that the presence of a non-canonical cysteine in Zf1 kinetically destabilizes the protein. Metal-exchange kinetics show that mutation of the cysteine establishes high-affinity coordination of the zinc. Our data indicate that selection of such a structurally destabilizing mutation during the course of evolution could present an opportunity for functional adaptation of the protein.
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32
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Influence of crowding agents on the dynamics of a multidomain protein in its denatured state: a solvation approach. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:289-305. [PMID: 32399581 DOI: 10.1007/s00249-020-01435-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 03/26/2020] [Accepted: 04/28/2020] [Indexed: 01/01/2023]
Abstract
It is now well appreciated that the crowded intracellular environment significantly modulates an array of physiological processes including protein folding-unfolding, aggregation, and dynamics to name a few. In this work we have studied the dynamics of domain I of the protein human serum albumin (HSA) in its urea-induced denatured states, in the presence of a series of commonly used macromolecular crowding agents. HSA was labeled at Cys-34 (a free cysteine) in domain I with the fluorophore 6-bromoacetyl-2-dimethylaminonaphthalene (BADAN) to act as a solvation probe. In partially denatured states (2-6 M urea), lower crowder concentrations (~ < 125 g/L) induced faster dynamics, while the dynamics became slower beyond 150 g/L of crowders. We propose that this apparent switch in dynamics is an evidence of a crossover from soft (enthalpic) to hard-core (entropic) interactions between the protein and crowder molecules. That soft interactions are also important for the crowders used here was further confirmed by the appreciable shift in the wavelength of the emission maximum of BADAN, in particular for PEG8000 and Ficoll 70 at concentrations where the excluded volume effect is not dominant.
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Guo J, Yang L, Gao Z, Zhao C, Mei Y, Song YY. Insight of MOF Environment-Dependent Enzyme Activity via MOFs-in-Nanochannels Configuration. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00591] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Junli Guo
- College of Sciences, Northeastern University, Shenyang 110004, China
| | - Lingling Yang
- College of Sciences, Northeastern University, Shenyang 110004, China
| | - Zhida Gao
- College of Sciences, Northeastern University, Shenyang 110004, China
| | - Chenxi Zhao
- College of Sciences, Northeastern University, Shenyang 110004, China
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Yan-Yan Song
- College of Sciences, Northeastern University, Shenyang 110004, China
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Molecular and macromolecular crowding-induced stabilization of proteins: Effect of dextran and its building block alone and their mixtures on stability and structure of lysozyme. Int J Biol Macromol 2020; 150:1238-1248. [DOI: 10.1016/j.ijbiomac.2019.10.135] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 10/13/2019] [Accepted: 10/14/2019] [Indexed: 11/22/2022]
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Interactions Under Crowding Milieu: Chemical-Induced Denaturation of Myoglobin is Determined by the Extent of Heme Dissociation on Interaction with Crowders. Biomolecules 2020; 10:biom10030490. [PMID: 32210191 PMCID: PMC7175338 DOI: 10.3390/biom10030490] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/06/2020] [Accepted: 03/08/2020] [Indexed: 12/13/2022] Open
Abstract
Generally, in vivo function and structural changes are studied by probing proteins in a dilute solution under in vitro conditions, which is believed to be mimicking proteins in intracellular milieu. Earlier, thermal-induced denaturation of myoglobin, in the milieu of crowder molecule showed destabilization of the metal protein. Destabilization of protein by thermal-induced denaturation involves a large extrapolation, so, the reliability is questionable. This led us to measure the effects of macromolecular crowding on its stability by chemical-induced denaturation of the protein using probes like circular dichroism and absorption spectroscopy in the presence of dextran 70 and ficoll 70 at various pHs (acidic: 6.0, almost neutral: 7.0 and basic: 8.0). Observations showed that the degree of destabilization of myoglobin was greater due to ficoll 70 as compared to that of dextran 70 so it can be understood that the nature of the crowder or the shape of the crowder has an important role towards the stability of proteins. Additionally, the degree of destabilization was observed as pH dependent, however the pH dependence is different for different crowders. Furthermore, isothermal titration calorimetry and molecular docking studies confirmed that both the crowders (ficoll and dextran) bind to heme moiety of myoglobin and a single binding site was observed for each.
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Parray ZA, Ahmad F, Alajmi MF, Hussain A, Hassan MI, Islam A. Formation of molten globule state in horse heart cytochrome c under physiological conditions: Importance of soft interactions and spectroscopic approach in crowded milieu. Int J Biol Macromol 2020; 148:192-200. [PMID: 31945437 DOI: 10.1016/j.ijbiomac.2020.01.119] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/07/2020] [Accepted: 01/12/2020] [Indexed: 11/17/2022]
Abstract
To understand protein folding problem under physiological condition, usually taken as dilute aqueous buffer at pH 7.0 and 25 °C, knowledge of properties of folding intermediates is important, such as molten globule (MG). We observed that polyethylene glycol 400 Da (PEG 400) induces molten globule state conformation in cytochrome c at pH 7.0 and 25 °C. This PEG-induced MG state has: (i) native tertiary structure partially perturbed, (ii) unperturbed native secondary structure, (iii) newly exposed hydrophobic patches, and (iv) has 1.58 times more hydrodynamic volume than that of the native protein. Isothermal titration calorimetry and docking studies showed specific binding between PEG 400 and cytochrome c. The study delineates that PEG-protein interactions are more complex than the excluded-volume. The soft interactions need to be seriously studied in crowding milieu that leads to destabilization of protein and overcome stabilizing exclusion volume effect. This study not only can help in unraveling the mystery of steps involved in the proper folding of proteins to solve the massively complicated problems of protein folding but also provides novel insights towards importance of structural change in proteins inside cell where intermediate states of protein import-export easily via membranes rather than native form of proteins.
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Affiliation(s)
- Zahoor Ahmad Parray
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Mohamed F Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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Werner T, Horvath I, Wittung-Stafshede P. Crosstalk Between Alpha-Synuclein and Other Human and Non-Human Amyloidogenic Proteins: Consequences for Amyloid Formation in Parkinson's Disease. JOURNAL OF PARKINSON'S DISEASE 2020; 10:819-830. [PMID: 32538869 PMCID: PMC7458506 DOI: 10.3233/jpd-202085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 05/13/2020] [Indexed: 02/07/2023]
Abstract
It was recently shown (Sampson et al., Elife9, 2020) that an amyloidogenic protein, CsgA, present in E. coli biofilms in the gut can trigger Parkinson's disease in mice. This study emphasizes the possible role of the gut microbiome in modulation (and even initiation) of human neurodegenerative disorders, such as Parkinson's disease. As the CsgA protein was found to accelerate alpha-synuclein (the key amyloidogenic protein in Parkinson's disease) amyloid formation in vitro, this result suggests that also other amyloidogenic proteins from gut bacteria, and even from the diet (such as stable allergenic proteins), may be able to affect human protein conformations and thereby modulate amyloid-related diseases. In this review, we summarize what has been reported in terms of in vitro cross-reactivity studies between alpha-synuclein and other amyloidogenic human and non-human proteins. It becomes clear from the limited data that exist that there is a fine line between acceleration and inhibition, but that cross-reactivity is widespread, and it is more common for other proteins (among the studied cases) to accelerate alpha-synuclein amyloid formation than to block it. It is of high importance to expand investigations of cross-reactivity between amyloidogenic proteins to both reveal underlying mechanisms and links between human diseases, as well as to develop new treatments that may be based on an altered gut microbiome.
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Affiliation(s)
- Tony Werner
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Istvan Horvath
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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Das N, Sen P. Size-dependent macromolecular crowding effect on the thermodynamics of protein unfolding revealed at the single molecular level. Int J Biol Macromol 2019; 141:843-854. [DOI: 10.1016/j.ijbiomac.2019.09.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/30/2019] [Accepted: 09/04/2019] [Indexed: 11/29/2022]
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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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Fernández C, Fodeke AA, Minton AP. Quantitative characterization of the concentration-dependent interaction between molecules of Dextran 70 in aqueous solution: Measurement and analysis in the context of thermodynamic and compressible sphere models. Biopolymers 2019; 110:e23284. [PMID: 31059131 PMCID: PMC6815238 DOI: 10.1002/bip.23284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/16/2019] [Accepted: 04/17/2019] [Indexed: 11/08/2022]
Abstract
The static light scattering and sedimentation equilibrium of solutions of Dextran 70 were measured as functions of concentration up to 100 g/L in pH 7.4 phosphate-buffered saline at temperatures between 5 and 37 °C. The concentration dependence of scattering intensity and the apparent molar mass obtained from sedimentation equilibrium were found to be nearly independent of temperature over this range to within the uncertainty of measurement. Global analysis of the concentration dependence of both properties yielded a reliable estimate of the concentration-dependent thermodynamic activity coefficient, a quantitative measure of the free energy of self-interaction. The self-interaction between Dextran molecules is compared with that of a globular protein (BSA) and a highly crosslinked polymer of similar molar mass (Ficoll 70). The observed concentration dependence of the free energy of Dextran self-interaction may be quantitatively accounted for by a semi-empirical model in which the polymer molecule is represented by a compressible sphere.
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Affiliation(s)
| | | | - Allen P. Minton
- Laboratory of Biochemistry & Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, United States Public Health Service, Bethesda MD 20892 USA
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Carbohydrate-Based Macromolecular Crowding-Induced Stabilization of Proteins: Towards Understanding the Significance of the Size of the Crowder. Biomolecules 2019; 9:biom9090477. [PMID: 31547256 PMCID: PMC6769620 DOI: 10.3390/biom9090477] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/02/2019] [Accepted: 09/06/2019] [Indexed: 11/23/2022] Open
Abstract
There are a large number of biomolecules that are accountable for the extremely crowded intracellular environment, which is totally different from the dilute solutions, i.e., the idealized conditions. Such crowded environment due to the presence of macromolecules of different sizes, shapes, and composition governs the level of crowding inside a cell. Thus, we investigated the effect of different sizes and shapes of crowders (ficoll 70, dextran 70, and dextran 40), which are polysaccharide in nature, on the thermodynamic stability, structure, and functional activity of two model proteins using UV-Vis spectroscopy and circular dichroism techniques. We observed that (a) the extent of stabilization of α-lactalbumin and lysozyme increases with the increasing concentration of the crowding agents due to the excluded volume effect and the small-sized and rod-shaped crowder, i.e., dextran 40 resulted in greater stabilization of both proteins than dextran 70 and ficoll 70; (b) structure of both the proteins remains unperturbed; and (c) enzymatic activity of lysozyme decreases with the increasing concentration of the crowder.
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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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Abstract
Copper is a redox-active transition metal ion required for the function of many essential human proteins. For biosynthesis of proteins coordinating copper, the metal may bind before, during or after folding of the polypeptide. If the metal binds to unfolded or partially folded structures of the protein, such coordination may modulate the folding reaction. The molecular understanding of how copper is incorporated into proteins requires descriptions of chemical, thermodynamic, kinetic and structural parameters involved in the formation of protein-metal complexes. Because free copper ions are toxic, living systems have elaborate copper-transport systems that include particular proteins that facilitate efficient and specific delivery of copper ions to target proteins. Therefore, these pathways become an integral part of copper protein folding in vivo. This review summarizes biophysical-molecular in vitro work assessing the role of copper in folding and stability of copper-binding proteins as well as protein-protein copper exchange reactions between human copper transport proteins. We also describe some recent findings about the participation of copper ions and copper proteins in protein misfolding and aggregation reactions in vitro.
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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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45
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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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Zegarra FC, Homouz D, Gasic AG, Babel L, Kovermann M, Wittung-Stafshede P, Cheung MS. Crowding-Induced Elongated Conformation of Urea-Unfolded Apoazurin: Investigating the Role of Crowder Shape in Silico. J Phys Chem B 2019; 123:3607-3617. [PMID: 30963769 DOI: 10.1021/acs.jpcb.9b00782] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Here, we show by solution nuclear magnetic resonance measurements that the urea-unfolded protein apoazurin becomes elongated when the synthetic crowding agent dextran 20 is present, in contrast to the prediction from the macromolecular crowding effect based on the argument of volume exclusion. To explore the complex interactions beyond volume exclusion, we employed coarse-grained molecular dynamics simulations to explore the conformational ensemble of apoazurin in a box of monodisperse crowders under strong chemically denaturing conditions. The elongated conformation of unfolded apoazurin appears to result from the interplay of the effective attraction between the protein and crowders and the shape of the crowders. With a volume-conserving crowder model, we show that the crowder shape provides an anisotropic direction of the depletion force, in which a bundle of surrounding rodlike crowders stabilize an elongated conformation of unfolded apoazurin in the presence of effective attraction between the protein and crowders.
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Affiliation(s)
- Fabio C Zegarra
- Department of Physics , University of Houston , Houston 77204 , United States
| | - Dirar Homouz
- Department of Physics , University of Houston , Houston 77204 , United States.,Department of Physics , Khalifa University of Science and Technology , Abu Dhabi , UAE.,Center for Theoretical Biological Physics , Rice University , Houston 77005 , United States
| | - Andrei G Gasic
- Department of Physics , University of Houston , Houston 77204 , United States.,Center for Theoretical Biological Physics , Rice University , Houston 77005 , United States
| | - Lucas Babel
- Department of Physics , University of Houston , Houston 77204 , United States
| | | | | | - Margaret S Cheung
- Department of Physics , University of Houston , Houston 77204 , United States.,Center for Theoretical Biological Physics , Rice University , Houston 77005 , United States
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Folding of poly-amino acids and intrinsically disordered proteins in overcrowded milieu induced by pH change. Int J Biol Macromol 2018; 125:244-255. [PMID: 30529354 DOI: 10.1016/j.ijbiomac.2018.12.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/27/2018] [Accepted: 12/02/2018] [Indexed: 12/24/2022]
Abstract
pH-induced structural changes of the synthetic homopolypeptides poly-E, poly-K, poly-R, and intrinsically disordered proteins (IDPs) prothymosin α (ProTα) and linker histone H1, in concentrated PEG solutions simulating macromolecular crowding conditions within the membrane-less organelles, were characterized. The conformational transitions of the studied poly-amino acids in the concentrated PEG solutions depend on the polymerization degree of these homopolypeptides, the size of their side chains, the charge distribution of the side chains, and the crowding agent concentration. The results obtained for poly-amino acids are valid for IDPs having a significant total charge. The overcrowded conditions promote a significant increase in the cooperativity of the pH-induced coil-α-helix transition of ProTα and provoke histone H1 aggregation. The most favorable conditions for the pH-induced structural transitions in concentrated PEG solutions are realized when the charged residues are grouped in blocks, and when the distance between the end of the side group carrying charge and the backbone is small. Therefore, the block-wise distribution of charged residues within the IDPs not only plays an important role in the liquid-liquid phase transitions, but may also define the expressivity of structural transitions of these proteins in the overcrowded conditions of the membrane-less organelles.
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Cheng K, Wu Q, Zhang Z, Pielak GJ, Liu M, Li C. Crowding and Confinement Can Oppositely Affect Protein Stability. Chemphyschem 2018; 19:3350-3355. [DOI: 10.1002/cphc.201800857] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Kai Cheng
- Key Laboratory of Magnetic Resonance in Biological Systems State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan Collaborative Innovation Center of Chemistry for Life Sciences, Wuhan Institute of Physics and Mathematics Chinese Academy of Sciences Wuhan 430071 P. R. China
| | - Qiong Wu
- Key Laboratory of Magnetic Resonance in Biological Systems State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan Collaborative Innovation Center of Chemistry for Life Sciences, Wuhan Institute of Physics and Mathematics Chinese Academy of Sciences Wuhan 430071 P. R. China
| | - Zeting Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan Collaborative Innovation Center of Chemistry for Life Sciences, Wuhan Institute of Physics and Mathematics Chinese Academy of Sciences Wuhan 430071 P. R. China
| | - Gary J. Pielak
- Department of Chemistry Department of Biochemistry and Biophysics University of North Carolina, Chapel Hill Chapel Hill, NC 27599-3290 USA
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan Collaborative Innovation Center of Chemistry for Life Sciences, Wuhan Institute of Physics and Mathematics Chinese Academy of Sciences Wuhan 430071 P. R. China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan Collaborative Innovation Center of Chemistry for Life Sciences, Wuhan Institute of Physics and Mathematics Chinese Academy of Sciences Wuhan 430071 P. R. China
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49
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Fonin AV, Darling AL, Kuznetsova IM, Turoverov KK, Uversky VN. Intrinsically disordered proteins in crowded milieu: when chaos prevails within the cellular gumbo. Cell Mol Life Sci 2018; 75:3907-3929. [PMID: 30066087 PMCID: PMC11105604 DOI: 10.1007/s00018-018-2894-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/24/2018] [Accepted: 07/26/2018] [Indexed: 12/18/2022]
Abstract
Effects of macromolecular crowding on structural and functional properties of ordered proteins, their folding, interactability, and aggregation are well documented. Much less is known about how macromolecular crowding might affect structural and functional behaviour of intrinsically disordered proteins (IDPs) or intrinsically disordered protein regions (IDPRs). To fill this gap, this review represents a systematic analysis of the available literature data on the behaviour of IDPs/IDPRs in crowded environment. Although it was hypothesized that, due to the excluded-volume effects present in crowded environments, IDPs/IDPRs would invariantly fold in the presence of high concentrations of crowding agents or in the crowded cellular environment, accumulated data indicate that, based on their response to the presence of crowders, IDPs/IDPRs can be grouped into three major categories, foldable, non-foldable, and unfoldable. This is because natural cellular environment is not simply characterized by the presence of high concentration of "inert" macromolecules, but represents an active milieu, components of which are engaged in direct physical interactions and soft interactions with target proteins. Some of these interactions with cellular components can cause (local) unfolding of query proteins. In other words, since crowding can cause both folding and unfolding of an IDP or its regions, the outputs of the placing of a query protein to the crowded environment would depend on the balance between these two processes. As a result, and because of the spatio-temporal heterogeneity in structural organization of IDPs, macromolecular crowding can differently affect structures of different IDPs. Recent studies indicate that some IDPs are able to undergo liquid-liquid-phase transitions leading to the formation of various proteinaceous membrane-less organelles (PMLOs). Although interiors of such PMLOs are self-crowded, being characterized by locally increased concentrations of phase-separating IDPs, these IDPs are minimally foldable or even non-foldable at all (at least within the physiologically safe time-frame of normal PMLO existence).
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Affiliation(s)
- Alexander V Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russian Federation
| | - April L Darling
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russian Federation
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russian Federation
- St. Petersburg State Polytechnical University, St. Petersburg, Russian Federation
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
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Kumar R, Kumar R, Sharma D, Garg M, Kumar V, Agarwal MC. Macromolecular crowding-induced molten globule states of the alkali pH-denatured proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:1102-1114. [DOI: 10.1016/j.bbapap.2018.08.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/07/2018] [Accepted: 08/30/2018] [Indexed: 11/26/2022]
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