1
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Liebau J, Laatsch BF, Rusnak J, Gunderson K, Finke B, Bargender K, Narkiewicz-Jodko A, Weeks K, Williams MT, Shulgina I, Musier-Forsyth K, Bhattacharyya S, Hati S. Polyethylene Glycol Impacts Conformation and Dynamics of Escherichia coli Prolyl-tRNA Synthetase Via Crowding and Confinement Effects. Biochemistry 2024; 63:1621-1635. [PMID: 38607680 PMCID: PMC11223479 DOI: 10.1021/acs.biochem.3c00719] [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: 12/19/2023] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024]
Abstract
Polyethylene glycol (PEG) is a flexible, nontoxic polymer commonly used in biological and medical research, and it is generally regarded as biologically inert. PEG molecules of variable sizes are also used as crowding agents to mimic intracellular environments. A recent study with PEG crowders revealed decreased catalytic activity of Escherichia coli prolyl-tRNA synthetase (Ec ProRS), where the smaller molecular weight PEGs had the maximum impact. The molecular mechanism of the crowding effects of PEGs is not clearly understood. PEG may impact protein conformation and dynamics, thus its function. In the present study, the effects of PEG molecules of various molecular weights and concentrations on the conformation and dynamics of Ec ProRS were investigated using a combined experimental and computational approach including intrinsic tryptophan fluorescence spectroscopy, atomic force microscopy, and atomistic molecular dynamic simulations. Results of the present study suggest that lower molecular weight PEGs in the dilute regime have modest effects on the conformational dynamics of Ec ProRS but impact the catalytic function primarily via the excluded volume effect; they form large clusters blocking the active site pocket. In contrast, the larger molecular weight PEGs in dilute to semidilute regimes have a significant impact on the protein's conformational dynamics; they wrap on the protein surface through noncovalent interactions. Thus, lower-molecular-weight PEG molecules impact protein dynamics and function via crowding effects, whereas larger PEGs induce confinement effects. These results have implications for the development of inhibitors for protein targets in a crowded cellular environment.
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Affiliation(s)
- Jessica Liebau
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Bethany F. Laatsch
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Joshua Rusnak
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Keegan Gunderson
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Brianna Finke
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Kassandra Bargender
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Alex Narkiewicz-Jodko
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Katelyn Weeks
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Murphi T. Williams
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Irina Shulgina
- Department
of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Karin Musier-Forsyth
- Department
of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sudeep Bhattacharyya
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Sanchita Hati
- Department
of Chemistry and Biochemistry, University
of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
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2
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Jordan JS, Lee KJ, Williams ER. Overcoming aggregation with laser heated nanoelectrospray mass spectrometry: thermal stability and pathways for loss of bicarbonate from carbonic anhydrase II. Analyst 2024; 149:2281-2290. [PMID: 38497240 DOI: 10.1039/d4an00229f] [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: 03/19/2024]
Abstract
Variable temperature electrospray mass spectrometry is useful for multiplexed measurements of the thermal stabilities of biomolecules, but the ionization process can be disrupted by aggregation-prone proteins/complexes that have irreversible unfolding transitions. Resistively heating solutions containing a mixture of bovine carbonic anhydrase II (BCAII), a CO2 fixing enzyme involved in many biochemical pathways, and cytochrome c leads to complete loss of carbonic anhydrase signal and a significant reduction in cytochrome c signal above ∼72 °C due to aggregation. In contrast, when the tips of borosilicate glass nanoelectrospray emitters are heated with a laser, complete thermal denaturation curves for both proteins are obtained in <1 minute. The simultaneous measurements of the melting temperature of BCAII and BCAII bound to bicarbonate reveal that the bicarbonate stabilizes the folded form of this protein by ∼6.4 °C. Moreover, the temperature dependences of different bicarbonate loss pathways are obtained. Although protein analytes are directly heated by the laser for only 140 ms, heat conduction further up the emitter leads to a total analyte heating time of ∼41 s. Pulsed laser heating experiments could reduce this time to ∼0.5 s for protein aggregation that occurs on a faster time scale. Laser heating provides a powerful method for studying the detailed mechanisms of cofactor/ligand loss with increasing temperature and promises a new tool for studying the effect of ligands, drugs, growth conditions, buffer additives, or other treatments on the stabilities of aggregation-prone biomolecules.
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Affiliation(s)
- Jacob S Jordan
- Department of Chemistry, University of California, Berkeley, California, 94720-1460, USA.
| | - Katherine J Lee
- Department of Chemistry, University of California, Berkeley, California, 94720-1460, USA.
| | - Evan R Williams
- Department of Chemistry, University of California, Berkeley, California, 94720-1460, USA.
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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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Chauhan M, Arshi SA, Narayanan N, Arfin HU, Sharma A. A mechanistic insight on how Compromised Hydrolysis of Triacylglycerol 7 (CHT7) restrains the involvement of it's CXC domain from quiescence repression. Int J Biol Macromol 2024; 265:130844. [PMID: 38484809 DOI: 10.1016/j.ijbiomac.2024.130844] [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: 01/24/2024] [Revised: 03/03/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
CHT7 is a regulator of quiescence repression in Chlamydomonas reinhardtii. Initially, CHT7's repression activity was thought to be managed by its DNA-binding CXC domain. Later, it was found that the CHT7-CXC domain is dispensable for CHT7's activities. Rather, CHT7's predicted protein domains were proposed to be involved in regulation activities by binding to other repressors in the cell. Yet, it remains unclear why and how CHT7 refrains its CXC domain from participating in any transcriptional activities. The question becomes more intriguing, since CXC binding regions are available in promoter regions of some of the misregulated genes in CHT7 mutant (cht7). Through biophysical experiments and molecular dynamics approaches, we studied the DNA recognition behavior of CHT7-CXC. The results indicate that this domain possesses sequence selectivity due to the differential binding abilities of its subdomains. Further, to understand if the case is that CXC loses its DNA binding capabilities in the vicinity of other repressors, we examined CHT7-CXC's DNA binding stability under the spatial constraint conditions created through fusing CHT7-CXC with AsLOV2. The results show limited ability of CHT7-CXC to withstand steric forces and provide insights to why and how algal cells may hold back CHT7-CXC's indulgence in quiescence repression. CLASSIFICATIONS: Biological Sciences, Biophysics and Computational Biology.
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Affiliation(s)
- Manisha Chauhan
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi 110025, India
| | - Syeda Amna Arshi
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi 110025, India
| | - Naveen Narayanan
- Regional Centre for Biotechnology, NCR-Cluster Faridabad, Haryana 121001, India
| | - Haseeb Ul Arfin
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi 110025, India
| | - Amit Sharma
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi 110025, India.
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5
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Alfano C, Fichou Y, Huber K, Weiss M, Spruijt E, Ebbinghaus S, De Luca G, Morando MA, Vetri V, Temussi PA, Pastore A. Molecular Crowding: The History and Development of a Scientific Paradigm. Chem Rev 2024; 124:3186-3219. [PMID: 38466779 PMCID: PMC10979406 DOI: 10.1021/acs.chemrev.3c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/13/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024]
Abstract
It is now generally accepted that macromolecules do not act in isolation but "live" in a crowded environment, that is, an environment populated by numerous different molecules. The field of molecular crowding has its origins in the far 80s but became accepted only by the end of the 90s. In the present issue, we discuss various aspects that are influenced by crowding and need to consider its effects. This Review is meant as an introduction to the theme and an analysis of the evolution of the crowding concept through time from colloidal and polymer physics to a more biological perspective. We introduce themes that will be more thoroughly treated in other Reviews of the present issue. In our intentions, each Review may stand by itself, but the complete collection has the aspiration to provide different but complementary perspectives to propose a more holistic view of molecular crowding.
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Affiliation(s)
- Caterina Alfano
- Structural
Biology and Biophysics Unit, Fondazione
Ri.MED, 90100 Palermo, Italy
| | - Yann Fichou
- CNRS,
Bordeaux INP, CBMN UMR 5248, IECB, University
of Bordeaux, F-33600 Pessac, France
| | - Klaus Huber
- Department
of Chemistry, University of Paderborn, 33098 Paderborn, Germany
| | - Matthias Weiss
- Experimental
Physics I, Physics of Living Matter, University
of Bayreuth, 95440 Bayreuth, Germany
| | - Evan Spruijt
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Simon Ebbinghaus
- Lehrstuhl
für Biophysikalische Chemie and Research Center Chemical Sciences
and Sustainability, Research Alliance Ruhr, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Giuseppe De Luca
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Valeria Vetri
- Dipartimento
di Fisica e Chimica − Emilio Segrè, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Annalisa Pastore
- King’s
College London, Denmark
Hill Campus, SE5 9RT London, United Kingdom
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6
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Pop-Jordanova N. Internet/Video Gaming: The Relevance of a New Phenomenon in the Youth. Pril (Makedon Akad Nauk Umet Odd Med Nauki) 2024; 45:5-12. [PMID: 38575381 DOI: 10.2478/prilozi-2024-0001] [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] [Indexed: 04/06/2024]
Abstract
The high level of technological growth in contemporary society, beside benefits, provokes different kinds of damages, especially among the worldwide youth population. World statistics have recognized that video and internet game addiction is a growing problem. In this context, it is supposed that 0.3 to 1.0 percent of the general population might be qualified as a potential sufferer of internet gaming disorder. However, youth between 18-34 years are the highest risk population. New research has shown the need of early identification of at-risk young people for internet addiction. Adverse experience in children of different forms of stress, negative life circumstances and especially negative, hostile parenting can lead to depression, social and cultural problems, together with significant boredom and loneliness levels. These are all confirmed to be related with addictive behaviour. Some neural correlates are discussed as the possible background of game addiction. Finally, therapeutic possibilities are presented.
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7
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Zhong-Johnson EZL, Dong Z, Canova CT, Destro F, Cañellas M, Hoffman MC, Maréchal J, Johnson TM, Zheng M, Schlau-Cohen GS, Lucas MF, Braatz RD, Sprenger KG, Voigt CA, Sinskey AJ. Analysis of Poly(ethylene terephthalate) degradation kinetics of evolved IsPETase variants using a surface crowding model. J Biol Chem 2024; 300:105783. [PMID: 38395309 PMCID: PMC10963241 DOI: 10.1016/j.jbc.2024.105783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/10/2024] [Accepted: 02/19/2024] [Indexed: 02/25/2024] Open
Abstract
Poly(ethylene terephthalate) (PET) is a major plastic polymer utilized in the single-use and textile industries. The discovery of PET-degrading enzymes (PETases) has led to an increased interest in the biological recycling of PET in addition to mechanical recycling. IsPETase from Ideonella sakaiensis is a candidate catalyst, but little is understood about its structure-function relationships with regards to PET degradation. To understand the effects of mutations on IsPETase productivity, we develop a directed evolution assay to identify mutations beneficial to PET film degradation at 30 °C. IsPETase also displays enzyme concentration-dependent inhibition effects, and surface crowding has been proposed as a causal phenomenon. Based on total internal reflectance fluorescence microscopy and adsorption experiments, IsPETase is likely experiencing crowded conditions on PET films. Molecular dynamics simulations of IsPETase variants reveal a decrease in active site flexibility in free enzymes and reduced probability of productive active site formation in substrate-bound enzymes under crowding. Hence, we develop a surface crowding model to analyze the biochemical effects of three hit mutations (T116P, S238N, S290P) that enhanced ambient temperature activity and/or thermostability. We find that T116P decreases susceptibility to crowding, resulting in higher PET degradation product accumulation despite no change in intrinsic catalytic rate. In conclusion, we show that a macromolecular crowding-based biochemical model can be used to analyze the effects of mutations on properties of PETases and that crowding behavior is a major property to be targeted for enzyme engineering for improved PET degradation.
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Affiliation(s)
| | - Ziyue Dong
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado, USA
| | - Christopher T Canova
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Francesco Destro
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Mikaila C Hoffman
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jeanne Maréchal
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; AgroParisTech, Palaiseau, France
| | - Timothy M Johnson
- Plasma Science and Fusion Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Maya Zheng
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Gabriela S Schlau-Cohen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Richard D Braatz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kayla G Sprenger
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Anthony J Sinskey
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
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8
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Nayar D. Molecular Crowders Can Induce Collapse in Hydrophilic Polymers via Soft Attractive Interactions. J Phys Chem B 2023. [PMID: 37410958 DOI: 10.1021/acs.jpcb.3c01319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
A comprehensive understanding of protein folding and biomolecular self-assembly in the intracellular environment requires obtaining a microscopic view of the crowding effects. The classical view of crowding explains biomolecular collapse in such an environment in terms of the entropic solvent excluded volume effects subjected to hard-core repulsions exerted by the inert crowders, neglecting their soft chemical interactions. In this study, the effects of nonspecific, soft interactions of molecular crowders in regulating the conformational equilibrium of hydrophilic (charged) polymers are examined. Using advanced molecular dynamics simulations, collapse free energies of an uncharged, a negatively charged, and a charge-neutral 32-mer generic polymer are computed. The strength of the polymer-crowder dispersion energy is modulated to examine its effect on polymer collapse. The results show that the crowders preferentially adsorb and drive the collapse of all three polymers. The uncharged polymer collapse is opposed by the change in solute-solvent interaction energy but is overcompensated by the favorable change in the solute-solvent entropy as observed in hydrophobic collapse. However, the negatively charged polymer collapses with a favorable change in solute-solvent interaction energy due to reduction in the dehydration energy penalty as the crowders partition to the polymer interface and shield the charged beads. The collapse of a charge-neutral polymer is opposed by the solute-solvent interaction energy but is overcompensated by the solute-solvent entropy change. However, for the strongly interacting crowders, the overall energetic penalty decreases since the crowders interact with polymer beads via cohesive bridging attractions to induce polymer collapse. These bridging attractions are found to be sensitive to the binding sites of the polymer, since they are absent in the negatively charged or uncharged polymers. These interesting differences in thermodynamic driving forces highlight the crucial role of the chemical nature of the macromolecule as well as of the crowder in determining the conformational equilibria in a crowded milieu. The results emphasize that the chemical interactions of the crowders should be explicitly considered to account for the crowding effects. The findings have implications in understanding the crowding effects on the protein free energy landscapes.
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Affiliation(s)
- Divya Nayar
- Department of Materials Science and Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
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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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Dutta P, Roy P, Sengupta N. Effects of External Perturbations on Protein Systems: A Microscopic View. ACS OMEGA 2022; 7:44556-44572. [PMID: 36530249 PMCID: PMC9753117 DOI: 10.1021/acsomega.2c06199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Protein folding can be viewed as the origami engineering of biology resulting from the long process of evolution. Even decades after its recognition, research efforts worldwide focus on demystifying molecular factors that underlie protein structure-function relationships; this is particularly relevant in the era of proteopathic disease. A complex co-occurrence of different physicochemical factors such as temperature, pressure, solvent, cosolvent, macromolecular crowding, confinement, and mutations that represent realistic biological environments are known to modulate the folding process and protein stability in unique ways. In the current review, we have contextually summarized the substantial efforts in unveiling individual effects of these perturbative factors, with major attention toward bottom-up approaches. Moreover, we briefly present some of the biotechnological applications of the insights derived from these studies over various applications including pharmaceuticals, biofuels, cryopreservation, and novel materials. Finally, we conclude by summarizing the challenges in studying the combined effects of multifactorial perturbations in protein folding and refer to complementary advances in experiment and computational techniques that lend insights to the emergent challenges.
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Affiliation(s)
- Pallab Dutta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
| | - Priti Roy
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma74078, United States
| | - Neelanjana Sengupta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
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11
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Irukuvajjula SS, Reddy JG, Vadrevu R. Crowding by Poly(ethylene glycol) Destabilizes Chemotaxis Protein Y (CheY). Biochemistry 2022; 61:1431-1443. [PMID: 35796609 DOI: 10.1021/acs.biochem.2c00030] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The prevailing understanding of various aspects of biochemical processes, including folding, stability, intermolecular interactions, and the binding of metals, substrates, and inhibitors, is derived from studies carried out under dilute and homogeneous conditions devoid of a crowding-related environment. The effect of crowding-induced modulation on the structure and stability of native and magnesium-dependent Chemotaxis Y (CheY), a bacterial signaling protein, was probed in the presence and absence of poly(ethylene glycol) (PEG). A combined analysis from circular dichroism, intrinsic and extrinsic fluorescence, and tryptophan fluorescence lifetime changes indicates that PEG perturbs the structure but leaves the thermal stability largely unchanged. Intriguingly, while the stability of the protein is enhanced in the presence of magnesium under dilute buffer conditions, PEG-induced crowding leads to reduced thermal stability in the presence of magnesium. Nuclear magnetic resonance (NMR) chemical shift perturbations and resonance broadening for a subset of residues indicate that PEG interacts specifically with a subset of hydrophilic and hydrophobic residues found predominantly in α helices, β strands, and in the vicinity of the metal-binding region. Thus, PEG prompted conformational perturbation, presumably provides a different situation for magnesium interaction, thereby perturbing the magnesium-prompted stability. In summary, our results highlight the dominance of enthalpic contributions between PEG and CheY via both hydrophilic and hydrophobic interactions, which can subtly affect the conformation, modulating the metal-protein interaction and stability, implying that in the context of cellular situation, structure, stability, and magnesium binding thermodynamics of CheY may be different from those measured in dilute solution.
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Affiliation(s)
- Shivkumar Sharma Irukuvajjula
- Department of Biological Sciences, Birla Institute of Technology & Science─Pilani, Hyderabad Campus, Jawahar Nagar, Shamirpet, Hyderabad 500078, India
| | - Jithender G Reddy
- NMR Division, Department of Analytical & Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Ministry of Science and Technology, Uppal Road, Tarnaka, Hyderabad 500007, India
| | - Ramakrishna Vadrevu
- Department of Biological Sciences, Birla Institute of Technology & Science─Pilani, Hyderabad Campus, Jawahar Nagar, Shamirpet, Hyderabad 500078, India
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12
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Harastani M, Eltsov M, Leforestier A, Jonic S. TomoFlow: Analysis of Continuous Conformational Variability of Macromolecules in Cryogenic Subtomograms based on 3D Dense Optical Flow. J Mol Biol 2021; 434:167381. [PMID: 34848215 DOI: 10.1016/j.jmb.2021.167381] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 01/14/2023]
Abstract
Cryogenic Electron Tomography (cryo-ET) allows structural and dynamics studies of macromolecules in situ. Averaging different copies of imaged macromolecules is commonly used to obtain their structure at higher resolution and discrete classification to analyze their dynamics. Instrumental and data processing developments are progressively equipping cryo-ET studies with the ability to escape the trap of classification into a complete continuous conformational variability analysis. In this work, we propose TomoFlow, a method for analyzing macromolecular continuous conformational variability in cryo-ET subtomograms based on a three-dimensional dense optical flow (OF) approach. The resultant lower-dimensional conformational space allows generating movies of macromolecular motion and obtaining subtomogram averages by grouping conformationally similar subtomograms. The animations and the subtomogram group averages reveal accurate trajectories of macromolecular motion based on a novel mathematical model that makes use of OF properties. This paper describes TomoFlow with tests on simulated datasets generated using different techniques, namely Normal Mode Analysis and Molecular Dynamics Simulation. It also shows an application of TomoFlow on a dataset of nucleosomes in situ, which provided promising results coherent with previous findings using the same dataset but without imposing any prior knowledge on the analysis of the conformational variability. The method is discussed with its potential uses and limitations.
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Affiliation(s)
- Mohamad Harastani
- IMPMC - UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France; Laboratoire de Physique des Solides (LPS), UMR 8502 CNRS, Université Paris-Saclay, Orsay, France. https://twitter.com/moh_harastani
| | - Mikhail Eltsov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, Illkirch, France. https://twitter.com/EltsovMikhail
| | - Amélie Leforestier
- Laboratoire de Physique des Solides (LPS), UMR 8502 CNRS, Université Paris-Saclay, Orsay, France
| | - Slavica Jonic
- IMPMC - UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France.
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13
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Lecinski S, Shepherd JW, Frame L, Hayton I, MacDonald C, Leake MC. Investigating molecular crowding during cell division and hyperosmotic stress in budding yeast with FRET. CURRENT TOPICS IN MEMBRANES 2021; 88:75-118. [PMID: 34862033 PMCID: PMC7612257 DOI: 10.1016/bs.ctm.2021.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Cell division, aging, and stress recovery triggers spatial reorganization of cellular components in the cytoplasm, including membrane bound organelles, with molecular changes in their compositions and structures. However, it is not clear how these events are coordinated and how they integrate with regulation of molecular crowding. We use the budding yeast Saccharomyces cerevisiae as a model system to study these questions using recent progress in optical fluorescence microscopy and crowding sensing probe technology. We used a Förster Resonance Energy Transfer (FRET) based sensor, illuminated by confocal microscopy for high throughput analyses and Slimfield microscopy for single-molecule resolution, to quantify molecular crowding. We determine crowding in response to cellular growth of both mother and daughter cells, in addition to osmotic stress, and reveal hot spots of crowding across the bud neck in the burgeoning daughter cell. This crowding might be rationalized by the packing of inherited material, like the vacuole, from mother cells. We discuss recent advances in understanding the role of crowding in cellular regulation and key current challenges and conclude by presenting our recent advances in optimizing FRET-based measurements of crowding while simultaneously imaging a third color, which can be used as a marker that labels organelle membranes. Our approaches can be combined with synchronized cell populations to increase experimental throughput and correlate molecular crowding information with different stages in the cell cycle.
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Affiliation(s)
- Sarah Lecinski
- Department of Physics, University of York, York, United Kingdom
| | - Jack W Shepherd
- Department of Physics, University of York, York, United Kingdom; Department of Biology, University of York, York, United Kingdom
| | - Lewis Frame
- School of Natural Sciences, University of York, York, United Kingdom
| | - Imogen Hayton
- Department of Biology, University of York, York, United Kingdom
| | - Chris MacDonald
- Department of Biology, University of York, York, United Kingdom
| | - Mark C Leake
- Department of Physics, University of York, York, United Kingdom; Department of Biology, University of York, York, United Kingdom.
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14
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Reduced efficacy of a Src kinase inhibitor in crowded protein solution. Nat Commun 2021; 12:4099. [PMID: 34215742 PMCID: PMC8253829 DOI: 10.1038/s41467-021-24349-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 06/14/2021] [Indexed: 12/22/2022] Open
Abstract
The inside of a cell is highly crowded with proteins and other biomolecules. How proteins express their specific functions together with many off-target proteins in crowded cellular environments is largely unknown. Here, we investigate an inhibitor binding with c-Src kinase using atomistic molecular dynamics (MD) simulations in dilute as well as crowded protein solution. The populations of the inhibitor, 4-amino-5-(4-methylphenyl)-7-(t-butyl)pyrazolo[3,4-d]pyrimidine (PP1), in bulk solution and on the surface of c-Src kinase are reduced as the concentration of crowder bovine serum albumins (BSAs) increases. This observation is consistent with the reduced PP1 inhibitor efficacy in experimental c-Src kinase assays in addition with BSAs. The crowded environment changes the major binding pathway of PP1 toward c-Src kinase compared to that in dilute solution. This change is explained based on the population shift mechanism of local conformations near the inhibitor binding site in c-Src kinase.
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15
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Deshwal A, Maiti S. Macromolecular Crowding Effect on the Activity of Liposome-Bound Alkaline Phosphatase: A Paradoxical Inhibitory Action. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:7273-7284. [PMID: 34086469 DOI: 10.1021/acs.langmuir.1c01177] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The cytoplasm of a cell is extremely crowded, with 20-30% being large biomolecules. This crowding enforces a significant amount of the physical and chemical barrier around biomolecules, so understanding any biomolecular event within the cellular system is challenging. Unsurprisingly, enzymes show a diverse kind of catalytic behavior inside a crowded environment and thus have remained an area of active interest in the last few decades. The situation can become even more complex and exciting in the case of understanding the behavior of a membrane-bound enzyme (almost 25-30% of enzymes are membrane-bound) in such a crowded environment that until now has remained unexplored. Herein, we have particularly investigated how a membrane-bound enzyme (using liposome-bound alkaline phosphatase) can behave in a crowded environment comprising polymer molecule-like poly(ethylene glycol) (PEG) of different weights (PEG400, PEG4000, and PEG9000) and Ficoll 400. We have compared the activity using a polymer microbead conjugated enzyme and have found that liposome-bound alkaline phosphatase had much higher activity in crowded environments, showing the importance and superiority of soft-deformable particles (i.e., vesicles) over hard spheres in macro-molecularly crowded media. Interstingly, we have found a paradoxical behavior of inhibitors in terms of both their extent and pathway of inhibitory action. For instance, phosphates, known as competitive inhibitors in buffer, behave as uncompetitive inhibitors in liposome-bound enzymes in crowded media with an ∼5-fold less inhibitory effect, whereas phenyl alanine (an uncompetitive inhibitor in buffer) did not show any inhibitory potential when the enzyme was membrane-bound and in crowded media containing PEG9000 (30 wt %). Overall, this demonstration elucidates aspects of membrane-bound enzymes in crowded media in terms of both catalytic behavior and inhibitory actions and can lead to further studies of the understanding of enzymatic behavior in such complex crowded environments having a dampening effect in regular diffusive transport.
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Affiliation(s)
- Akshi Deshwal
- Indian Institute of Science Education and Research (IISER) Mohali, Department of Chemical Sciences, Knowledge City, Manauli 140306, India
| | - Subhabrata Maiti
- Indian Institute of Science Education and Research (IISER) Mohali, Department of Chemical Sciences, Knowledge City, Manauli 140306, India
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16
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Bolaños K, Celis F, Garrido C, Campos M, Guzmán F, Kogan MJ, Araya E. Adsorption of bovine serum albumin on gold nanoprisms: interaction and effect of NIR irradiation on protein corona. J Mater Chem B 2021; 8:8644-8657. [PMID: 32842142 DOI: 10.1039/d0tb01246g] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Because of their photothermal properties, gold nanoparticles (AuNPs) have gained attention regarding their use in drug delivery and therapeutic applications. In this sense, it is interesting to consider their interactions with biologically available proteins, such as serum albumin, as well as the effects of irradiation and photothermal conversion on the protein structure that can lead to a loss of function or generate an immune response. Gold nanoprisms (AuNPrs) have gained interest due to their low toxicity, ease of synthesis, and excellent stability, promoting their use in bioapplications such as surface-enhanced Raman spectroscopy (SERS), drug delivery, and photothermal therapy. The interaction between AuNPrs, with plasmon bands centred in the near-infrared region (NIR), and bovine serum albumin (BSA) has not been explored yet. UV-Vis spectroscopy, dynamic light scattering (DLS) and fluorescence spectroscopy were used to study the interaction between AuNPrs and BSA in addition to estimation of the adsorption rate and kinetic and thermodynamic parameters (K, ΔH°, ΔG°, ΔS°, and Ea) using adsorption isotherms and Langmuir and Freundlich models. The results suggest spontaneous cooperative binding in multilayer adsorption, achieved by the chemisorption of BSA on the AuNPr surface through the S-Au interaction, as confirmed by Raman spectroscopy. On the other hand, the photothermal conversion efficiency (PE) of the coated nanoparticles after NIR irradiation was assessed, resulting in a slight decrease in the PE of BSA coated on AuNPrs in comparison with that of noncapped nanoparticles. The effect of the irradiation on the protein conformation of capped nanoparticles was also assessed; circular dichroism showed BSA unfolding upon interaction with AuNPrs, with a decrease in the α-helix and β-sheet contents, as well as an increase in random coil conformations. Changes in the Raman spectrum suggest a modification of the disposition of the protein residues exposed to the gold surface after NIR irradiation; but at the secondary structure level, no relevant changes were observed. This provides possibilities for the use of NPs-BSA for bioapplications based on the photothermal effect promoted by laser irradiation, since the biological identity of the protein is preserved after NIR irradiation.
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Affiliation(s)
- Karen Bolaños
- Doctorado en Fisicoquímica Molecular, Facultad de Ciencias Exactas, Universidad Andres Bello, Av. Republica 275, Santiago, Chile and Departamento de Química Farmacológica y Toxicológica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santos Dumont 964, Independencia, Santiago, Chile. and Advanced Center for Chronic Diseases (ACCDiS), Santos Dumont 964, Independencia, Santiago, Chile
| | - Freddy Celis
- Laboratorio de Procesos Fotónicos y Electroquímicos, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Casilla 34-V, Valparaíso, Chile
| | - Carlos Garrido
- Departamento de Química, Facultad de Ciencias Básicas, Universidad Metropolitana de Ciencias de la Educación, Av. José Pedro Alessandri 774, Ñuñoa, Santiago, Chile
| | - Marcelo Campos
- Department of Chemistry, Faculty of Sciences, University of Chile, P. O. Box 653, Santiago, Chile
| | - Fanny Guzmán
- Núcleo de Biotecnología Curauma, Pontifcia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Marcelo J Kogan
- Departamento de Química Farmacológica y Toxicológica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santos Dumont 964, Independencia, Santiago, Chile. and Advanced Center for Chronic Diseases (ACCDiS), Santos Dumont 964, Independencia, Santiago, Chile
| | - Eyleen Araya
- Advanced Center for Chronic Diseases (ACCDiS), Santos Dumont 964, Independencia, Santiago, Chile and Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Av. Republica 275, Santiago, Chile.
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17
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Basak S, Sakia N, Dougherty L, Guo Z, Wu F, Mindlin F, Lary JW, Cole JL, Ding F, Bowen ME. Probing Interdomain Linkers and Protein Supertertiary Structure In Vitro and in Live Cells with Fluorescent Protein Resonance Energy Transfer. J Mol Biol 2021; 433:166793. [PMID: 33388290 DOI: 10.1016/j.jmb.2020.166793] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 12/03/2020] [Accepted: 12/21/2020] [Indexed: 12/23/2022]
Abstract
Many proteins are composed of independently-folded domains connected by flexible linkers. The primary sequence and length of such linkers can set the effective concentration for the tethered domains, which impacts rates of association and enzyme activity. The length of such linkers can be sensitive to environmental conditions, which raises questions as to how studies in dilute buffer relate to the highly-crowded cellular environment. To examine the role of linkers in domain separation, we measured Fluorescent Protein-Fluorescence Resonance Energy Transfer (FP-FRET) for a series of tandem FPs that varied in the length of their interdomain linkers. We used discrete molecular dynamics to map the underlying conformational distribution, which revealed intramolecular contact states that we confirmed with single molecule FRET. Simulations found that attached FPs increased linker length and slowed conformational dynamics relative to the bare linkers. This makes the CLYs poor sensors of inherent linker properties. However, we also showed that FP-FRET in CLYs was sensitive to solvent quality and macromolecular crowding making them potent environmental sensors. Finally, we targeted the same proteins to the plasma membrane of living mammalian cells to measure FP-FRET in cellulo. The measured FP-FRET when tethered to the plasma membrane was the same as that in dilute buffer. While caveats remain regarding photophysics, this suggests that the supertertiary conformational ensemble of these CLY proteins may not be affected by this specific cellular environment.
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Affiliation(s)
- Sujit Basak
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Nabanita Sakia
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634-0978, USA
| | - Laura Dougherty
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Zhuojun Guo
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Fang Wu
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Frank Mindlin
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Jeffrey W Lary
- National Analytical Ultracentrifugation Facility, University of Connecticut, Storrs, CT 06269, USA
| | - James L Cole
- National Analytical Ultracentrifugation Facility, University of Connecticut, Storrs, CT 06269, USA; Department of Molecular and Cell Biology, and Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634-0978, USA
| | - Mark E Bowen
- Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA.
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18
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Nayar D. Small crowder interactions can drive hydrophobic polymer collapse as well as unfolding. Phys Chem Chem Phys 2020; 22:18091-18101. [PMID: 32760995 DOI: 10.1039/d0cp02402c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Biomolecules evolve and function in the intracellular crowded environment that is densely packed with macromolecules. Yet, a microscopic understanding of the effects of such an environment on the conformational preferences of biomolecules remains elusive. While prior investigations have attributed crowding effects mainly to the excluded volume (size) effects of the crowders, very little is known about the effects exerted due to their chemical interactions. In this study, crowding effects of tri-alanine peptides on the collapse equilibria of generic hydrophobic polymer are investigated using molecular dynamics simulations. The role of weak, non-specific, attractive polymer-crowder interactions in modulating the polymer collapse equilibria is examined. The results highlight that crowding effects can lead to polymer compaction as well as unfolding depending on the strength of polymer-crowder interaction energy. Strongly interacting crowders weaken hydrophobic collapse (or unfold the polymer) at high volume fractions and induce polymer collapse only under dilute conditions. Weakly interacting crowders induce polymer collapse at all crowder concentrations. Interestingly, the thermodynamic driving forces for polymer collapse are remarkably different in the two cases. Strongly and weakly interacting crowders induce collapse by preferential adsorption and preferential depletion respectively. The findings provide new insights into the possible effects of interplay of intermolecular interactions in a crowded environment. The results have implications in understanding the impact of crowding in altering free energy landscapes of proteins.
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Affiliation(s)
- Divya Nayar
- Centre for Computational and Data Sciences, Indian Institute of Technology Kharagpur, West Bengal 721302, India.
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19
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Yuan Y, Zhu Q, Song R, Ma J, Dong H. A Two-Ended Data-Driven Accelerated Sampling Method for Exploring the Transition Pathways between Two Known States of Protein. J Chem Theory Comput 2020; 16:4631-4640. [PMID: 32320614 DOI: 10.1021/acs.jctc.9b01184] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Conformational transitions of protein between different states are often associated with their biological functions. These dynamic processes, however, are usually not easy to be well characterized by experimental measurements, mainly because of inadequate temporal and spatial resolution. Meantime, sampling of configuration space with molecular dynamics (MD) simulations is still a challenge. Here we proposed a robust two-ended data-driven accelerated (teDA2) conformational sampling method, which drives the structural change in an adaptively updated feature space without introducing a bias potential. teDA2 was applied to explore adenylate kinase (ADK), a model with well characterized "open" and "closed" states. A single conformational transition event of ADK could be achieved within only a few or tens of nanoseconds sampled with teDA2. By analyzing hundreds of transition events, we reproduced different mechanisms and the associated pathways for domain motion of ADK reported in the literature. The multiroute characteristic of ADK was confirmed by the fact that some metastable states identified with teDA2 resemble available crystal structures determined at different conditions. This feature was further validated with Markov state modeling with independent MD simulations. Therefore, our work provides strong evidence for the conformational plasticity of protein, which is mainly due to the inherent degree of flexibility. As a reliable and efficient enhanced sampling protocol, teDA2 could be used to study the dynamics between functional states of various biomolecular machines.
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Affiliation(s)
- Yigao Yuan
- Kuang Yaming Honors School, Nanjing University, 210023 Nanjing, China
| | - Qiang Zhu
- Kuang Yaming Honors School, Nanjing University, 210023 Nanjing, China.,Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing China
| | - Ruiheng Song
- Kuang Yaming Honors School, Nanjing University, 210023 Nanjing, China
| | - Jing Ma
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing China
| | - Hao Dong
- Kuang Yaming Honors School, Nanjing University, 210023 Nanjing, China.,Institute for Brain Sciences, Nanjing University, Nanjing 210023, China
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20
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Adams LM, Andrews RJ, Hu QH, Schmit HL, Hati S, Bhattacharyya S. Crowder-Induced Conformational Ensemble Shift in Escherichia coli Prolyl-tRNA Synthetase. Biophys J 2019; 117:1269-1284. [PMID: 31542226 PMCID: PMC6818166 DOI: 10.1016/j.bpj.2019.08.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/27/2019] [Accepted: 08/28/2019] [Indexed: 01/08/2023] Open
Abstract
The effect of molecular crowding on the structure and function of Escherichia coli prolyl-transfer RNA synthetase (Ec ProRS), a member of the aminoacyl-transfer RNA synthetase family, has been investigated using a combined experimental and theoretical method. Ec ProRS is a multidomain enzyme; coupled-domain dynamics are essential for efficient catalysis. To gain insight into the mechanistic detail of the crowding effect, kinetic studies were conducted with varying concentrations and sizes of crowders. In parallel, spectroscopic and quantum chemical studies were employed to probe the "soft interactions" between crowders and protein side chains. Finally, the dynamics of the dimeric protein was examined in the presence of crowders using a long-duration (70 ns) classical molecular dynamic simulations. The results of the simulations revealed a shift in the conformational ensemble, which is consistent with the preferential exclusion of cosolutes. The "soft interactions" model of the crowding effect also explained the alteration in kinetic parameters. In summary, the study found that the effects of molecular crowding on both conformational dynamics and catalytic function are correlated in the multidomain Ec ProRS, an enzyme that is central to protein synthesis in all living cells. This study affirmed that large and small cosolutes have considerable impacts on the structure, dynamics, and function of modular proteins and therefore must be considered for stabilizing protein-based pharmaceuticals and industrial enzymes.
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Affiliation(s)
- Lauren M Adams
- Department of Chemistry, University of Wisconsin at Eau Claire, Eau Claire, Wisconsin
| | - Ryan J Andrews
- Department of Chemistry, University of Wisconsin at Eau Claire, Eau Claire, Wisconsin
| | - Quin H Hu
- Department of Chemistry, University of Wisconsin at Eau Claire, Eau Claire, Wisconsin
| | - Heidi L Schmit
- Department of Chemistry, University of Wisconsin at Eau Claire, Eau Claire, Wisconsin
| | - Sanchita Hati
- Department of Chemistry, University of Wisconsin at Eau Claire, Eau Claire, Wisconsin.
| | - Sudeep Bhattacharyya
- Department of Chemistry, University of Wisconsin at Eau Claire, Eau Claire, Wisconsin.
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21
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Enzymatic activity of human immunodeficiency virus type 1 protease in crowded solutions. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:685-689. [PMID: 31463540 PMCID: PMC6742607 DOI: 10.1007/s00249-019-01392-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/27/2019] [Accepted: 08/12/2019] [Indexed: 11/02/2022]
Abstract
Cells are crowded with various macromolecules and metabolites, which affect biochemical reactions in many ways, from the diffusion of substrates to catalytic activities of enzymes. We herein investigated the proteolytic activity of the human immunodeficiency virus type 1 protease (HIV-1 PR) under non-crowded and crowded conditions. The latter environment was mimicked with various (poly)ethylene glycol molecules as crowding agents. We found that these crowding agents affect the kinetic parameters of the HIV-1 PR catalyzed reaction by increasing the Michaelis-Menten constant and decreasing the maximum velocity. The influence of crowding was concentration dependent. We explain this effect by the dynamics of the HIV-1 PR flexible flaps that cover the peptide substrate binding site and are crucial for enzyme activity, and by a possibly slower substrate-enzyme association time in the crowded conditions.
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22
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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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23
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Ghosh A, Smith PES, Qin S, Yi M, Zhou HX. Both Ligands and Macromolecular Crowders Preferentially Bind to Closed Conformations of Maltose Binding Protein. Biochemistry 2019; 58:2208-2217. [PMID: 30950267 DOI: 10.1021/acs.biochem.9b00154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In cellular environments, proteins not only interact with their specific partners but also encounter a high concentration of bystander macromolecules, or crowders. Nonspecific interactions with macromolecular crowders modulate the activities of proteins, but our knowledge about the rules of nonspecific interactions is still very limited. In previous work, we presented experimental evidence that macromolecular crowders acted competitively in inhibiting the binding of maltose binding protein (MBP) with its ligand maltose. Competition between a ligand and an inhibitor may result from binding to either the same site or different conformations of the protein. Maltose binds to the cleft between two lobes of MBP, and in a series of mutants, the affinities increased with an increase in the extent of lobe closure. Here we investigated whether macromolecular crowders also have a conformational or site preference when binding to MBP. The affinities of a polymer crowder, Ficoll70, measured by monitoring tryptophan fluorescence were 3-6-fold higher for closure mutants than for wild-type MBP. Competition between the ligand and crowder, as indicated by fitting of titration data and directly by nuclear magnetic resonance spectroscopy, and their similar preferences for closed MBP conformations further suggest the scenario in which the crowder, like maltose, preferentially binds to the interlobe cleft of MBP. Similar observations were made for bovine serum albumin as a protein crowder. Conformational and site preferences in MBP-crowder binding allude to the paradigm that nonspecific interactions can possess hallmarks of molecular recognition, which may be essential for intracellular organizations including colocalization of proteins and liquid-liquid phase separation.
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Affiliation(s)
- Archishman Ghosh
- Institute of Molecular Biophysics , Florida State University , Tallahassee , Florida 30306 , United States.,Department of Chemistry and Department of Physics , University of Illinois at Chicago , Chicago , Illinois 60607 , United States
| | - Pieter E S Smith
- Institute of Molecular Biophysics , Florida State University , Tallahassee , Florida 30306 , United States
| | - Sanbo Qin
- Institute of Molecular Biophysics , Florida State University , Tallahassee , Florida 30306 , United States.,Department of Chemistry and Department of Physics , University of Illinois at Chicago , Chicago , Illinois 60607 , United States
| | - Myunggi Yi
- Department of Biomedical Engineering , Pukyong National University , Busan 48513 , South Korea
| | - Huan-Xiang Zhou
- Institute of Molecular Biophysics , Florida State University , Tallahassee , Florida 30306 , United States.,Department of Chemistry and Department of Physics , University of Illinois at Chicago , Chicago , Illinois 60607 , United States
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24
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Macromolecular crowding and membrane binding proteins: The case of phospholipase A1. Chem Phys Lipids 2019; 218:91-102. [DOI: 10.1016/j.chemphyslip.2018.12.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 10/10/2018] [Accepted: 12/13/2018] [Indexed: 11/24/2022]
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25
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Nguemaha V, Qin S, Zhou HX. Atomistic Modeling of Intrinsically Disordered Proteins Under Polyethylene Glycol Crowding: Quantitative Comparison with Experimental Data and Implication of Protein-Crowder Attraction. J Phys Chem B 2018; 122:11262-11270. [PMID: 30230839 DOI: 10.1021/acs.jpcb.8b07066] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The malleability of intrinsically disordered proteins (IDPs) has generated great interest in understanding how their conformations respond to crowded cellular environments. Experiments can report gross properties such as fluorescence resonance energy transfer (FRET) efficiency but cannot resolve the conformational ensembles of IDPs and their interactions with macromolecular crowders. Computation can in principle provide the latter information but in practice has been hampered by the enormous expense for realistic modeling of IDPs and crowders and for sufficient conformational sampling. Here, taking advantage of a powerful method called FMAP (fast Fourier transform-based modeling of atomistic protein-crowder interactions), we computed how the conformational ensembles of three IDPs are modified in concentrated polyethylene glycol (PEG) 6000 solutions. We represented the IDPs at the all-atom level and the PEG molecules at a coarse-grained level and calculated the experimental observable, i.e., FRET efficiency. Whereas accounting for only steric repulsion of PEG led to overestimation of crowding effects, quantitative agreement with experimental data was obtained upon including mild IDP-PEG attraction. The present work demonstrates that realistic modeling of IDPs under crowded conditions for direct comparison with experiments is now achievable.
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Affiliation(s)
- Valery Nguemaha
- Department of Physics and Institute of Molecular Biophysics , Florida State University , Tallahassee , Florida 32306 , United States
| | - Sanbo Qin
- Department of Physics and Institute of Molecular Biophysics , Florida State University , Tallahassee , Florida 32306 , United States
| | - Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics , Florida State University , Tallahassee , Florida 32306 , United States.,Department of Chemistry and Department of Physics , University of Illinois at Chicago , Chicago , Illinois 60607 , United States
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26
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Kumar R, Sharma D, Kumar V, Kumar R. Factors defining the effects of macromolecular crowding on dynamics and thermodynamic stability of heme proteins in-vitro. Arch Biochem Biophys 2018; 654:146-162. [DOI: 10.1016/j.abb.2018.07.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 11/28/2022]
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27
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Biswas S, Kundu J, Mukherjee SK, Chowdhury PK. Mixed Macromolecular Crowding: A Protein and Solvent Perspective. ACS OMEGA 2018; 3:4316-4330. [PMID: 30023892 PMCID: PMC6044960 DOI: 10.1021/acsomega.7b01864] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/16/2018] [Indexed: 06/08/2023]
Abstract
In the living cell, biomolecules perform their respective functions in the presence of not only one type of macromolecules but rather in the presence of various macromolecules with different shapes and sizes. In this study, we have investigated the effects of five single macromolecular crowding agents, Dextran 6, Dextran 40, Dextran 70, Ficoll 70, and PEG 8000 and their binary mixtures on the modulation in the domain separation of human serum albumin using a Förster resonance energy transfer-based approach and the translational mobility of a small fluorescent probe fluorescein isothiocyanate (FITC) using fluorescence correlation spectroscopy (FCS). Our observations suggest that mixed crowding induces greater cooperativity in the domain movement as compared to the components of the mixtures. Thermodynamic analyses of the same provide evidence of crossovers from enthalpy-based interactions to effects dominated by hard-sphere potential. When compared with those obtained for individual crowders, both domain movements and FITC diffusion studies show significant deviations from ideality, with an ideal solution being considered to be that arising from the sum of the contributions of those obtained in the presence of individual crowding agents. Considering the fact that domain movements are local (on the order of a few angstroms) in nature while translational movements span much larger lengthscales, our results imply that the observed deviation from simple additivity exists at several possible levels or lengthscales in such mixtures. Moreover, the nature and the type of deviation not only depend on the identities of the components of the crowder mixtures but are also influenced by the particular face of the serum protein (either the domain I-II or the domain II-III face) that the crowders interact with, thus providing further insights into the possible existence of microheterogeneities in such solutions.
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28
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Singh P, Choudhury S, Dutta S, Adhikari A, Bhattacharya S, Pal D, Pal SK. Ultrafast spectroscopy on DNA-cleavage by endonuclease in molecular crowding. Int J Biol Macromol 2017; 103:395-402. [DOI: 10.1016/j.ijbiomac.2017.05.058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/14/2017] [Indexed: 10/19/2022]
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29
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Xu G, Zhao J, Cheng K, Wu Q, Liu X, Liu M, Li C. The Effects of Macromolecular Crowding on Calmodulin Structure and Function. Chemistry 2017; 23:6736-6740. [DOI: 10.1002/chem.201700367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Indexed: 02/07/2023]
Affiliation(s)
- Guohua Xu
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P. R. China
| | - Jiajing Zhao
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P. R. China
- Graduate University of Chinese Academy of Sciences; Beijing 100029 P. R. China
| | - Kai Cheng
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P. R. China
- Graduate University of Chinese Academy of Sciences; Beijing 100029 P. R. China
| | - Qiong Wu
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P. R. China
| | - Xiaoli Liu
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P. R. China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P. R. China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; National Center for Magnetic Resonance in Wuhan; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan 430071 P. R. China
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30
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Li J, Hu Z, Beuerman R, Verma C. Molecular Environment Modulates Conformational Differences between Crystal and Solution States of Human β-Defensin 2. J Phys Chem B 2017; 121:2739-2747. [DOI: 10.1021/acs.jpcb.7b00083] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jianguo Li
- Singapore Eye Research Institute, 11 Third Hospital Avenue, #06-00, Singapore 168751
- Bioinformatics Institute (A*-STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Zhongqiao Hu
- Bioinformatics Institute (A*-STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Roger Beuerman
- Singapore Eye Research Institute, 11 Third Hospital Avenue, #06-00, Singapore 168751
- Department
of Ophthalmology, National University of Singapore, Singapore 119074
- School of
Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459
| | - Chandra Verma
- Singapore Eye Research Institute, 11 Third Hospital Avenue, #06-00, Singapore 168751
- Bioinformatics Institute (A*-STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
- School
of Biological Sciences, Nanyang Technological University, Singapore 637551
- Department
of Biological Sciences, National University of Singapore, Singapore 117543
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31
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Shahid S, Hassan MI, Islam A, Ahmad F. Size-dependent studies of macromolecular crowding on the thermodynamic stability, structure and functional activity of proteins: in vitro and in silico approaches. Biochim Biophys Acta Gen Subj 2017; 1861:178-197. [DOI: 10.1016/j.bbagen.2016.11.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 11/09/2016] [Accepted: 11/10/2016] [Indexed: 11/27/2022]
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32
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Celaya G, Fernández-Higuero JA, Martin I, Rivas G, Moro F, Muga A. Crowding Modulates the Conformation, Affinity, and Activity of the Components of the Bacterial Disaggregase Machinery. J Mol Biol 2016; 428:2474-2487. [DOI: 10.1016/j.jmb.2016.04.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 04/18/2016] [Accepted: 04/20/2016] [Indexed: 12/13/2022]
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33
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Huang KY, Kingsley CN, Sheil R, Cheng CY, Bierma JC, Roskamp KW, Khago D, Martin RW, Han S. Stability of Protein-Specific Hydration Shell on Crowding. J Am Chem Soc 2016; 138:5392-402. [PMID: 27052457 PMCID: PMC7849722 DOI: 10.1021/jacs.6b01989] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate that the effect of protein crowding is critically dependent on the stability of the protein's hydration shell, which can dramatically vary between different proteins. In the human eye lens, γS-crystallin (γS-WT) forms a densely packed transparent hydrogel with a high refractive index, making it an ideal system for studying the effects of protein crowding. A single point mutation generates the cataract-related variant γS-G18V, dramatically altering the optical properties of the eye lens. This system offers an opportunity to explore fundamental questions regarding the effect of protein crowding, using γS-WT and γS-G18V: (i) how do the diffusion dynamics of hydration water change as a function of protein crowding?; and (ii) upon hydrogel formation of γS-WT, has a dynamic transition occurred generating a single population of hydration water, or do populations of bulk and hydration water coexist? Using localized spin probes, we separately probe the local translational diffusivity of both surface hydration and interstitial water of γS-WT and γS-G18V in solution. Surprisingly, we find that under the influence of hydrogel formation at highly crowded γS-WT concentrations up to 500 mg/mL, the protein hydration shell remains remarkably dynamic, slowing by less than a factor of 2, if at all, compared to that in dilute protein solutions of ∼5 mg/mL. Upon self-crowding, the population of this robust surface hydration water increases, while a significant bulk-like water population coexists even at ∼500 mg/mL protein concentrations. In contrast, surface water of γS-G18V irreversibly dehydrates with moderate concentration increases or subtle alterations to the solution conditions, demonstrating that the effect of protein crowding is highly dependent on the stability of the protein-specific hydration shell. The core function of γS-crystallin in the eye lens may be precisely its capacity to preserve a robust hydration shell, whose stability is abolished by a single G18V mutation.
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Affiliation(s)
- Kuo-Ying Huang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106
| | | | - Ryan Sheil
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106
| | - Chi-Yuan Cheng
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106
| | - Jan C. Bierma
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697
| | - Kyle W. Roskamp
- Department of Chemistry, University of California, Irvine, CA 92697
| | - Domarin Khago
- Department of Chemistry, University of California, Irvine, CA 92697
| | - Rachel W. Martin
- Department of Chemistry, University of California, Irvine, CA 92697
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106
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34
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Unusual effects of crowders on heme retention in myoglobin. FEBS Lett 2015; 589:3807-15. [DOI: 10.1016/j.febslet.2015.11.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 11/05/2015] [Accepted: 11/10/2015] [Indexed: 11/24/2022]
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35
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Schneider SH, Lockwood SP, Hargreaves DI, Slade DJ, LoConte MA, Logan BE, McLaughlin EE, Conroy MJ, Slade KM. Slowed Diffusion and Excluded Volume Both Contribute to the Effects of Macromolecular Crowding on Alcohol Dehydrogenase Steady-State Kinetics. Biochemistry 2015; 54:5898-906. [DOI: 10.1021/acs.biochem.5b00533] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Samuel H. Schneider
- Department
of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Schuyler P. Lockwood
- Department
of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Dominique I. Hargreaves
- Department
of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - David J. Slade
- Department
of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Micaela A. LoConte
- Department
of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Bridget E. Logan
- Department
of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Erin E. McLaughlin
- Department
of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Michael J. Conroy
- Department
of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
| | - Kristin M. Slade
- Department
of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, United States
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36
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Alvarez FJD, Orelle C, Huang Y, Bajaj R, Everly RM, Klug CS, Davidson AL. Full engagement of liganded maltose-binding protein stabilizes a semi-open ATP-binding cassette dimer in the maltose transporter. Mol Microbiol 2015; 98:878-94. [PMID: 26268698 DOI: 10.1111/mmi.13165] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2015] [Indexed: 01/31/2023]
Abstract
MalFGK2 is an ATP-binding cassette (ABC) transporter that mediates the uptake of maltose/maltodextrins into Escherichia coli. A periplasmic maltose-binding protein (MBP) delivers maltose to the transmembrane subunits (MalFG) and stimulates the ATPase activity of the cytoplasmic nucleotide-binding subunits (MalK dimer). This MBP-stimulated ATPase activity is independent of maltose for purified transporter in detergent micelles. However, when the transporter is reconstituted in membrane bilayers, only the liganded form of MBP efficiently stimulates its activity. To investigate the mechanism of maltose stimulation, electron paramagnetic resonance spectroscopy was used to study the interactions between the transporter and MBP in nanodiscs and in detergent. We found that full engagement of both lobes of maltose-bound MBP unto MalFGK2 is facilitated by nucleotides and stabilizes a semi-open MalK dimer. Maltose-bound MBP promotes the transition to the semi-open state of MalK when the transporter is in the membrane, whereas such regulation does not require maltose in detergent. We suggest that stabilization of the semi-open MalK2 conformation by maltose-bound MBP is key to the coupling of maltose transport to ATP hydrolysis in vivo, because it facilitates the progression of the MalK dimer from the open to the semi-open conformation, from which it can proceed to hydrolyze ATP.
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Affiliation(s)
| | - Cédric Orelle
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Yan Huang
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Ruchika Bajaj
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - R Michael Everly
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Candice S Klug
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Amy L Davidson
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
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37
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Abstract
Oxygen is transported throughout the body by hemoglobin (Hb) in red blood cells (RBCs). Although the oxygen affinity of blood is well-understood and routinely assessed in patients by pulse oximetry, variability at the single-cell level has not been previously measured. In contrast, single-cell measurements of RBC volume and Hb concentration are taken millions of times per day by clinical hematology analyzers, and they are important factors in determining the health of the hematologic system. To better understand the variability and determinants of oxygen affinity on a cellular level, we have developed a system that quantifies the oxygen saturation, cell volume, and Hb concentration for individual RBCs in high throughput. We find that the variability in single-cell saturation peaks at an oxygen partial pressure of 2.9%, which corresponds to the maximum slope of the oxygen-Hb dissociation curve. In addition, single-cell oxygen affinity is positively correlated with Hb concentration but independent of osmolarity, which suggests variation in the Hb to 2,3-diphosphoglycerate (2-3 DPG) ratio on a cellular level. By quantifying the functional behavior of a cellular population, our system adds a dimension to blood cell analysis and other measurements of single-cell variability.
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38
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Majumder S, Xue J, DeMott CM, Reverdatto S, Burz DS, Shekhtman A. Probing protein quinary interactions by in-cell nuclear magnetic resonance spectroscopy. Biochemistry 2015; 54:2727-38. [PMID: 25894651 DOI: 10.1021/acs.biochem.5b00036] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Historically introduced by McConkey to explain the slow mutation rate of highly abundant proteins, weak protein (quinary) interactions are an emergent property of living cells. The protein complexes that result from quinary interactions are transient and thus difficult to study biochemically in vitro. Cross-correlated relaxation-induced polarization transfer-based in-cell nuclear magnetic resonance allows the characterization of protein quinary interactions with atomic resolution inside live prokaryotic and eukaryotic cells. We show that RNAs are an important component of protein quinary interactions. Protein quinary interactions are unique to the target protein and may affect physicochemical properties, protein activity, and interactions with drugs.
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Affiliation(s)
- Subhabrata Majumder
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Jing Xue
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Christopher M DeMott
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Sergey Reverdatto
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - David S Burz
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
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39
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Goldenberg DP, Argyle B. Minimal effects of macromolecular crowding on an intrinsically disordered protein: a small-angle neutron scattering study. Biophys J 2014; 106:905-14. [PMID: 24559993 DOI: 10.1016/j.bpj.2013.12.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 11/26/2013] [Accepted: 12/02/2013] [Indexed: 01/04/2023] Open
Abstract
Small-angle neutron scattering was used to study the effects of macromolecular crowding by two globular proteins, i.e., bovine pancreatic trypsin inhibitor and equine metmyoglobin, on the conformational ensemble of an intrinsically disordered protein, the N protein of bacteriophage λ. The λ N protein was uniformly labeled with (2)H, and the concentrations of D2O in the samples were adjusted to match the neutron scattering contrast of the unlabeled crowding proteins, thereby masking their contribution to the scattering profiles. Scattering from the deuterated λ N was recorded for samples containing up to 0.12 g/mL bovine pancreatic trypsin inhibitor or 0.2 g/mL metmyoglobin. The radius of gyration of the uncrowded protein was estimated to be 30 Å and was found to be remarkably insensitive to the presence of crowders, varying by <2 Å for the highest crowder concentrations. The scattering profiles were also used to estimate the fractal dimension of λ N, which was found to be ∼1.8 in the absence or presence of crowders, indicative of a well-solvated and expanded random coil under all of the conditions examined. These results are contrary to the predictions of theoretical treatments and previous experimental studies demonstrating compaction of unfolded proteins by crowding with polymers such as dextran and Ficoll. A computational simulation suggests that some previous treatments may have overestimated the effective volumes of disordered proteins and the variation of these volumes within an ensemble. The apparent insensitivity of λ N to crowding may also be due in part to weak attractive interactions with the crowding proteins, which may compensate for the effects of steric exclusion.
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Affiliation(s)
| | - Brian Argyle
- Department of Biology, University of Utah, Salt Lake City, Utah
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40
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Sterpone F, Melchionna S, Tuffery P, Pasquali S, Mousseau N, Cragnolini T, Chebaro Y, St-Pierre JF, Kalimeri M, Barducci A, Laurin Y, Tek A, Baaden M, Nguyen PH, Derreumaux P. The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. Chem Soc Rev 2014; 43:4871-93. [PMID: 24759934 PMCID: PMC4426487 DOI: 10.1039/c4cs00048j] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows the study of single protein properties, DNA-RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we first review the current state of the model and the most exciting applications using advanced conformational sampling methods. We then present the current limitations and a perspective on the ongoing developments.
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Affiliation(s)
- Fabio Sterpone
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris, France.
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41
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Seyler SL, Beckstein O. Sampling large conformational transitions: adenylate kinase as a testing ground. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.919497] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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42
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Qin S, Zhou HX. Further Development of the FFT-based Method for Atomistic Modeling of Protein Folding and Binding under Crowding: Optimization of Accuracy and Speed. J Chem Theory Comput 2014; 10:2824-2835. [PMID: 25061446 PMCID: PMC4095916 DOI: 10.1021/ct5001878] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Indexed: 12/21/2022]
Abstract
![]()
Recently,
we (Qin, S.; Zhou, H. X. J. Chem. Theory Comput.2013, 9, 4633–4643) developed
the FFT-based method for Modeling Atomistic Proteins–crowder interactions, henceforth FMAP. Given its potential
wide use for calculating effects of crowding on protein folding and
binding free energies, here we aimed to optimize the accuracy and
speed of FMAP. FMAP is based on expressing protein–crowder
interactions as correlation functions and evaluating the latter via
fast Fourier transform (FFT). The numerical accuracy of FFT improves
as the grid spacing for discretizing space is reduced, but at increasing
computational cost. We sought to speed up FMAP calculations by using
a relatively coarse grid spacing of 0.6 Å and then correcting
for discretization errors. This strategy was tested for different
types of interactions (hard-core repulsion, nonpolar attraction, and
electrostatic interaction) and over a wide range of protein–crowder
systems. We were able to correct for the numerical errors on hard-core
repulsion and nonpolar attraction by an 8% inflation of atomic hard-core
radii and on electrostatic interaction by a 5% inflation of the magnitudes
of protein atomic charges. The corrected results have higher accuracy
and enjoy a speedup of more than 100-fold over those obtained using
a fine grid spacing of 0.15 Å. With this optimization of accuracy
and speed, FMAP may become a practical tool for realistic modeling
of protein folding and binding in cell-like environments.
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Affiliation(s)
- Sanbo Qin
- Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida, United States
| | - Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida, United States
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43
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Balcells C, Pastor I, Vilaseca E, Madurga S, Cascante M, Mas F. Macromolecular crowding effect upon in vitro enzyme kinetics: mixed activation-diffusion control of the oxidation of NADH by pyruvate catalyzed by lactate dehydrogenase. J Phys Chem B 2014; 118:4062-8. [PMID: 24660904 DOI: 10.1021/jp4118858] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Enzyme kinetics studies have been usually designed as dilute solution experiments, which differ substantially from in vivo conditions. However, cell cytosol is crowded with a high concentration of molecules having different shapes and sizes. The consequences of such crowding in enzymatic reactions remain unclear. The aim of the present study is to understand the effect of macromolecular crowding produced by dextran of different sizes and at diverse concentrations in the well-known reaction of oxidation of NADH by pyruvate catalyzed by L-lactate dehydrogenase (LDH). Our results indicate that the reaction rate is determined by both the occupied volume and the relative size of dextran obstacles with respect to the enzyme present in the reaction. Moreover, we analyzed the influence of macromolecular crowding on the Michaelis-Menten constants, vmax and Km. The obtained results show that only high concentrations and large sizes of dextran reduce both constants suggesting a mixed activation-diffusion control of this enzymatic reaction due to the dextran crowding action. From our knowledge, this is the first experimental study that depicts mixed activation-diffusion control in an enzymatic reaction due to the effect of crowding.
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Affiliation(s)
- Cristina Balcells
- Department of Physical Chemistry and Research Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona (UB) , 08028 Barcelona, Spain
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44
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Xu G, Ye Y, Liu X, Cao S, Wu Q, Cheng K, Liu M, Pielak GJ, Li C. Strategies for Protein NMR in Escherichia coli. Biochemistry 2014; 53:1971-81. [DOI: 10.1021/bi500079u] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Guohua Xu
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Yansheng Ye
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- Graduate University of Chinese Academy of Sciences, Beijing 100029, P. R. China
| | - Xiaoli Liu
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Shufen Cao
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
Center for Magnetic Resonance, 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,
Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Kai Cheng
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- Graduate University of Chinese Academy of Sciences, Beijing 100029, P. R. China
| | - Maili Liu
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Gary J. Pielak
- Department
of Chemistry and Department of Biochemistry and Biophysics, University of North Carolina−Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Conggang Li
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
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45
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Schaupp A, Sabet O, Dudanova I, Ponserre M, Bastiaens P, Klein R. The composition of EphB2 clusters determines the strength in the cellular repulsion response. ACTA ACUST UNITED AC 2014; 204:409-22. [PMID: 24469634 PMCID: PMC3912530 DOI: 10.1083/jcb.201305037] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Graded responses to cell–cell repulsion signals mediated by Ephrin–Eph receptor interactions are specified by EphB2 cluster composition, such that the relative abundance of inactive dimers and active higher-order clusters determines the strength of the repulsive response. Trans interactions of erythropoietin-producing human hepatocellular (Eph) receptors with their membrane-bound ephrin ligands generate higher-order clusters that can form extended signaling arrays. The functional relevance of the cluster size for repulsive signaling is not understood. We used chemical dimerizers and fluorescence anisotropy to generate and visualize specific EphB2 cluster species in living cells. We find that cell collapse responses are induced by small-sized EphB2 clusters, suggesting that extended EphB2 arrays are dispensable and that EphB2 activation follows an ON–OFF switch with EphB2 dimers being inactive and trimers and tetramers being fully functional. Moreover, the strength of the collapse response is determined by the abundance of multimers over dimers within a cluster population: the more dimers are present, the weaker the response. Finally, we show that the C-terminal modules of EphB2 have negative regulatory effects on ephrin-induced clustering. These results shed new light on the mechanism and regulation of EphB2 activation and provide a model on how Eph signaling translates into graded cellular responses.
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Affiliation(s)
- Andreas Schaupp
- Department of Molecules - Signaling - Development, Max Planck Institute of Neurobiology, 82152 Martinsried, Germany
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46
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Pastor I, Pitulice L, Balcells C, Vilaseca E, Madurga S, Isvoran A, Cascante M, Mas F. Effect of crowding by Dextrans in enzymatic reactions. Biophys Chem 2014; 185:8-13. [DOI: 10.1016/j.bpc.2013.10.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 10/23/2013] [Accepted: 10/26/2013] [Indexed: 11/29/2022]
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47
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Nakano SI, Miyoshi D, Sugimoto N. Effects of molecular crowding on the structures, interactions, and functions of nucleic acids. Chem Rev 2013; 114:2733-58. [PMID: 24364729 DOI: 10.1021/cr400113m] [Citation(s) in RCA: 369] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Shu-ichi Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) and Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University , 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
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48
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Qin S, Zhou HX. Effects of Macromolecular Crowding on the Conformational Ensembles of Disordered Proteins. J Phys Chem Lett 2013; 4:10.1021/jz401817x. [PMID: 24312701 PMCID: PMC3846091 DOI: 10.1021/jz401817x] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Due to their conformational malleability, intrinsically disordered proteins (IDPs) are particularly susceptible to influences of crowded cellular environments. Here we report a computational study of the effects of macromolecular crowding on the conformational ensemble of a coarse-grained IDP model, by using two approaches. In one, the IDP is simulated along with the crowders; in the other, crowder-free simulations are postprocessed to predict the conformational ensembles under crowding. We found significant decreases in the radius of gyration of the IDP under crowding, and suggest repulsive interactions with crowders as a common cause for chain compaction in a number of experimental studies. The postprocessing approach accurately reproduced the conformational ensembles of the IDP in the direct simulations here, and holds enormous potential for realistic modeling of IDPs under crowding, by permitting thorough conformation sampling for the proteins even when they and the crowders are both represented at the all-atom level.
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Affiliation(s)
| | - Huan-Xiang Zhou
- Correspondence information: phone, (850) 645-1336; fax, (850) 644-7244; e-mail,
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49
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Competitive interactions of ligands and macromolecular crowders with maltose binding protein. PLoS One 2013; 8:e74969. [PMID: 24124463 PMCID: PMC3790770 DOI: 10.1371/journal.pone.0074969] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 08/09/2013] [Indexed: 01/22/2023] Open
Abstract
Cellular signaling involves a cascade of recognition events occurring in a complex environment with high concentrations of proteins, polysaccharides, and other macromolecules. The influence of macromolecular crowders on protein binding affinity through hard-core repulsion is well studied, and possible contributions of protein-crowder soft attraction have been implicated recently. Here we present direct evidence for weak association of maltose binding protein (MBP) with a polysaccharide crowder Ficoll, and that this association effectively competes with the binding of the natural ligand, maltose. Titration data over wide ranges of maltose and Ficoll concentrations fit well with a three-state competitive binding model. Broadening of MBP 1H15N TROSY spectra by the addition of Ficoll indicates weak protein-crowder association, and subsequent recovery of sharp NMR peaks upon addition of maltose indicates that the interactions of the crowder and the ligand with MBP are competitive. We hypothesize that, in the Escherichia coli periplasm, the competitive interactions of polysaccharides and maltose with MBP could allow MBP to shuttle between the peptidoglycan attached to the outer membrane and the ATP-binding cassette transporter in the inner membrane.
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50
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Qin S, Zhou HX. An FFT-based method for modeling protein folding and binding under crowding: benchmarking on ellipsoidal and all-atom crowders. J Chem Theory Comput 2013; 9. [PMID: 24187527 DOI: 10.1021/ct4005195] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
It is now well recognized that macromolecular crowding can exert significant effects on protein folding and binding stability. In order to calculate such effects in direct simulations of proteins mixed with bystander macromolecules, the latter (referred to as crowders) are usually modeled as spheres and the proteins represented at a coarse-grained level. Our recently developed postprocessing approach allows the proteins to be represented at the all-atom level but, for computational efficiency, has only been implemented for spherical crowders. Modeling crowder molecules in cellular environments and in vitro experiments as spheres may distort their effects on protein stability. Here we present a new method that is capable for treating aspherical crowders. The idea, borrowed from protein-protein docking, is to calculate the excess chemical potential of the proteins in crowded solution by fast Fourier transform (FFT). As the first application, we studied the effects of ellipsoidal crowders on the folding and binding free energies of all-atom proteins, and found, in agreement with previous direct simulations with coarse-grained protein models, that the aspherical crowders exert greater stabilization effects than spherical crowders of the same volume. Moreover, as demonstrated here, the FFT-based method has the important property that its computational cost does not increase strongly even when the level of details in representing the crowders is increased all the way to all-atom, thus significantly accelerating realistic modeling of protein folding and binding in cell-like environments.
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Affiliation(s)
- Sanbo Qin
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida
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