1
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Shirley JC, Baiz CR. MANUSCRIPT Local Crowd, Local Probe: Strengths and Drawbacks of Azidohomoalanine as a Site-Specific Crowding Probe. J Phys Chem B 2024; 128:5310-5319. [PMID: 38806061 DOI: 10.1021/acs.jpcb.4c00712] [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: 05/30/2024]
Abstract
Every residue on a protein can be characterized by its interaction with water, in lack or in excess, as water is the matrix of biological systems. Infrared spectroscopy and the implementation of local azidohomoalanine (AHA) probes allow us to move beyond an ensemble or surface-driven conceptualization of water behavior and toward a granular, site-specific picture. In this paper, we examined the role of crowding in modulating both global and local behavior on the β-hairpin, TrpZip2 using a combination of Fourier-transform infrared spectroscopy (FTIR) spectroscopy, two-dimensional infrared (2D IR) spectroscopy, and molecular dynamics simulations. We found that, at the amino acid level, crowding drove dehydration of both sheet and turn peptide sites as well as free AHA. However, the subpicosecond dynamics showed highly individualized responses based on the local environment. Interestingly, while steady-state FTIR measurements revealed similar responses at the amino-acid level to hard versus soft crowding (dehydration), we found that PEG and glucose had opposite stabilizing and destabilizing effects on the protein secondary structure, emphasizing an important distinction in understanding the impact of crowding on protein structure as well as the role of crowding across length scales.
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Affiliation(s)
- Joseph C Shirley
- Department of Chemistry, University of Texas, Austin 78712, Texas, United States
| | - Carlos R Baiz
- Department of Chemistry, University of Texas, Austin 78712, Texas, United States
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2
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Fink A, Fazliev S, Abele T, Spatz JP, Göpfrich K, Cavalcanti-Adam EA. Membrane localization of actin filaments stabilizes giant unilamellar vesicles against external deforming forces. Eur J Cell Biol 2024; 103:151428. [PMID: 38850712 DOI: 10.1016/j.ejcb.2024.151428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 05/25/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024] Open
Abstract
Actin organization is crucial for establishing cell polarity, which influences processes such as directed cell motility and division. Despite its critical role in living organisms, achieving similar polarity in synthetic cells remains challenging. In this study, we employ a bottom-up approach to investigate how molecular crowders facilitate the formation of cortex-like actin networks and how these networks localize and organize based on membrane shape. Using giant unilamellar vesicles (GUVs) as models for cell membranes, we show that actin filaments can arrange along the membrane to form cortex-like structures. Notably, this organization is achieved using only actin and crowders as a minimal set of components. We utilize surface micropatterning to examine actin filament organization in deformed GUVs adhered to various pattern shapes. Our findings indicate that at the periphery of spherical GUVs, actin bundles align along the membrane. However, in highly curved regions of adhered GUVs, actin bundles avoid crossing the highly curved edges perpendicular to the adhesion site and instead remain in the lower curved regions by aligning parallel to the micropatterned surface. Furthermore, the actin bundles increase the stiffness of the GUVs, effectively counteracting strong deformations when GUVs adhere to micropatterns. This finding is corroborated by real-time deformability cytometry on GUVs with synthetic actin cortices. By precisely manipulating the shape of GUVs, our study provides a minimal system to investigate the interplay between actin structures and the membrane. Our findings provide insights into the spatial organization of actin structures within crowded environments, specifically inside GUVs that resemble the size and shape of cells. This study advances our understanding of actin network organization and functionality within cell-sized compartments.
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Affiliation(s)
- Andreas Fink
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, Heidelberg 69120, Germany
| | - Sunnatullo Fazliev
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, Heidelberg 69120, Germany
| | - Tobias Abele
- Biophysical Engineering Group, Center for Molecular Biology of Heidelberg University (ZMBH) Heidelberg University, Im Neuenheimer Feld 329, Heidelberg 69120, Germany
| | - Joachim P Spatz
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, Heidelberg 69120, Germany
| | - Kerstin Göpfrich
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Jahnstraße 29, Heidelberg 69120, Germany; Biophysical Engineering Group, Center for Molecular Biology of Heidelberg University (ZMBH) Heidelberg University, Im Neuenheimer Feld 329, Heidelberg 69120, Germany
| | - Elisabetta Ada Cavalcanti-Adam
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, Heidelberg 69120, Germany; Cellular Biomechanics, University of Bayreuth, Universitätsstraße 30, Bayreuth 95447, Germany.
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3
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Rzycki M, Drabik D. Multifaceted Activity of Fabimycin: Insights from Molecular Dynamics Studies on Bacterial Membrane Models. J Chem Inf Model 2024; 64:4204-4217. [PMID: 38733348 PMCID: PMC11134499 DOI: 10.1021/acs.jcim.4c00228] [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: 02/08/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
Membranes─cells' essential scaffolds─are valid molecular targets for substances with an antimicrobial effect. While certain substances, such as octenidine, have been developed to target membranes for antimicrobial purposes, the recently reported molecule, fabimycin (F2B)─a novel agent targeting drug-resistant Gram-negative bacteria─has not received adequate attention regarding its activity on membranes in the literature. The following study aims to investigate the effects of F2B on different bacterial membrane models, including simple planar bilayers and more complex bilayer systems that mimic the Escherichia coli shell equipped with double inner and outer bilayers. Our results show that F2B exhibited more pronounced interactions with bacterial membrane systems compared to the control PC system. Furthermore, we observed significant changes in local membrane property homeostasis in both the inner and outer membrane models, specifically in the case of lateral diffusion, membrane thickness, and membrane resilience (compressibility, tilt). Finally, our results showed that the effect of F2B differed in a complex system and a single membrane system. Our study provides new insights into the multifaceted activity of F2B, demonstrating its potential to disrupt bacterial membrane homeostasis, indicating that its activity extends the currently known mechanism of FabI enzyme inhibition. This disruption, coupled with the ability of F2B to penetrate the outer membrane layers, sheds new light on the behavior of this antimicrobial molecule. This highlights the importance of the interaction with the membrane, crucial in combating bacterial infections, particularly those caused by drug-resistant strains.
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Affiliation(s)
- Mateusz Rzycki
- Department of Biomedical Engineering, Wroclaw University of Science and Technology, Wroclaw 50-370, Poland
| | - Dominik Drabik
- Department of Biomedical Engineering, Wroclaw University of Science and Technology, Wroclaw 50-370, Poland
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4
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Mukherjee S, Ramos S, Pezzotti S, Kalarikkal A, Prass TM, Galazzo L, Gendreizig D, Barbosa N, Bordignon E, Havenith M, Schäfer LV. Entropy Tug-of-War Determines Solvent Effects in the Liquid-Liquid Phase Separation of a Globular Protein. J Phys Chem Lett 2024; 15:4047-4055. [PMID: 38580324 PMCID: PMC11033941 DOI: 10.1021/acs.jpclett.3c03421] [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: 12/06/2023] [Revised: 02/15/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024]
Abstract
Liquid-liquid phase separation (LLPS) plays a key role in the compartmentalization of cells via the formation of biomolecular condensates. Here, we combined atomistic molecular dynamics (MD) simulations and terahertz (THz) spectroscopy to determine the solvent entropy contribution to the formation of condensates of the human eye lens protein γD-Crystallin. The MD simulations reveal an entropy tug-of-war between water molecules that are released from the protein droplets and those that are retained within the condensates, two categories of water molecules that were also assigned spectroscopically. A recently developed THz-calorimetry method enables quantitative comparison of the experimental and computational entropy changes of the released water molecules. The strong correlation mutually validates the two approaches and opens the way to a detailed atomic-level understanding of the different driving forces underlying the LLPS.
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Affiliation(s)
- Saumyak Mukherjee
- Center
for Theoretical Chemistry, Ruhr University
Bochum, D-44780 Bochum, Germany
| | - Sashary Ramos
- Department
of Physical Chemistry II, Ruhr University
Bochum, D-44780 Bochum, Germany
| | - Simone Pezzotti
- Department
of Physical Chemistry II, Ruhr University
Bochum, D-44780 Bochum, Germany
| | - Abhishek Kalarikkal
- Faculty
of Chemistry and Biochemistry, Ruhr University
Bochum, D-44780 Bochum, Germany
| | - Tobias M. Prass
- Center
for Theoretical Chemistry, Ruhr University
Bochum, D-44780 Bochum, Germany
| | - Laura Galazzo
- Faculty
of Chemistry and Biochemistry, Ruhr University
Bochum, D-44780 Bochum, Germany
| | - Dominik Gendreizig
- Department
of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, 1211 Geneva, Switzerland
| | - Natercia Barbosa
- Department
of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, 1211 Geneva, Switzerland
| | - Enrica Bordignon
- Faculty
of Chemistry and Biochemistry, Ruhr University
Bochum, D-44780 Bochum, Germany
- Department
of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, 1211 Geneva, Switzerland
| | - Martina Havenith
- Department
of Physical Chemistry II, Ruhr University
Bochum, D-44780 Bochum, Germany
| | - Lars V. Schäfer
- Center
for Theoretical Chemistry, Ruhr University
Bochum, D-44780 Bochum, Germany
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5
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Raczyłło E, Gołowicz D, Skóra T, Kazimierczuk K, Kondrat S. Size Sensitivity of Metabolite Diffusion in Macromolecular Crowds. NANO LETTERS 2024; 24. [PMID: 38607288 PMCID: PMC11057039 DOI: 10.1021/acs.nanolett.3c05100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/13/2024]
Abstract
Metabolites play crucial roles in cellular processes, yet their diffusion in the densely packed interiors of cells remains poorly understood, compounded by conflicting reports in existing studies. Here, we employ pulsed-gradient stimulated-echo NMR and Brownian/Stokesian dynamics simulations to elucidate the behavior of nano- and subnanometer-sized tracers in crowded environments. Using Ficoll as a crowder, we observe a linear decrease in tracer diffusivity with increasing occupied volume fraction, persisting─somewhat surprisingly─up to volume fractions of 30-40%. While simulations suggest a linear correlation between diffusivity slowdown and particle size, experimental findings hint at a more intricate relationship, possibly influenced by Ficoll's porosity. Simulations and numerical calculations of tracer diffusivity in the E. coli cytoplasm show a nonlinear yet monotonic diffusion slowdown with particle size. We discuss our results in the context of nanoviscosity and discrepancies with existing studies.
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Affiliation(s)
- Edyta Raczyłło
- Institute
of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
- Department
of Theoretical Chemistry, Institute of Chemical Sciences, Faculty
of Chemistry, Maria Curie-Skłodowska
University in Lublin, 20-031 Lublin, Poland
| | - Dariusz Gołowicz
- Institute
of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - Tomasz Skóra
- Institute
of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
- Scientific
Computing and Imaging Institute, University
of Utah, Salt Lake City, Utah 84112, United States
| | | | - Svyatoslav Kondrat
- Institute
of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
- Institute
for Computational Physics, University of
Stuttgart 70569, Stuttgart, Germany
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6
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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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7
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Hosseini AN, van der Spoel D. Martini on the Rocks: Can a Coarse-Grained Force Field Model Crystals? J Phys Chem Lett 2024; 15:1079-1088. [PMID: 38261634 PMCID: PMC10839907 DOI: 10.1021/acs.jpclett.4c00012] [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: 01/02/2024] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 01/25/2024]
Abstract
Computational chemistry is an important tool in numerous scientific disciplines, including drug discovery and structural biology. Coarse-grained models offer simple representations of molecular systems that enable simulations of large-scale systems. Because there has been an increase in the adoption of such models for simulations of biomolecular systems, critical evaluation is warranted. Here, the stability of the amyloid peptide and organic crystals is evaluated using the Martini 3 coarse-grained force field. The crystals change shape drastically during the simulations. Radial distribution functions show that the distance between backbone beads in β-sheets increases by ∼1 Å, breaking the crystals. The melting points of organic compounds are much too low in the Martini force field. This suggests that Martini 3 lacks the specific interactions needed to accurately simulate peptides or organic crystals without imposing artificial restraints. The problems may be exacerbated by the use of the 12-6 potential, suggesting that a softer potential could improve this model for crystal simulations.
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Affiliation(s)
- A. Najla Hosseini
- Department of Cell and Molecular
Biology, Uppsala University, Box 596, SE-75124 Uppsala, Sweden
| | - David van der Spoel
- Department of Cell and Molecular
Biology, Uppsala University, Box 596, SE-75124 Uppsala, Sweden
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8
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Kompella VPS, Romano MC, Stansfield I, Mancera RL. What determines sub-diffusive behavior in crowded protein solutions? Biophys J 2024; 123:134-146. [PMID: 38073154 PMCID: PMC10808025 DOI: 10.1016/j.bpj.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/07/2023] [Accepted: 12/04/2023] [Indexed: 12/22/2023] Open
Abstract
The aqueous environment inside cells is densely packed. A typical cell has a macromolecular concentration in the range 90-450 g/L, with 5%-40% of its volume being occupied by macromolecules, resulting in what is known as macromolecular crowding. The space available for the free diffusion of metabolites and other macromolecules is thus greatly reduced, leading to so-called excluded volume effects. The slow diffusion of macromolecules under crowded conditions has been explained using transient complex formation. However, sub-diffusion noted in earlier works is not well characterized, particularly the role played by transient complex formation and excluded volume effects. We have used Brownian dynamics simulations to characterize the diffusion of chymotrypsin inhibitor 2 in protein solutions of bovine serum albumin and lysozyme at concentrations ranging from 50 to 300 g/L. The predicted changes in diffusion coefficient as a function of crowder concentration are consistent with NMR experiments. The sub-diffusive behavior observed in the sub-microsecond timescale can be explained in terms of a so-called cage effect, arising from rattling motion in a local molecular cage as a consequence of excluded volume effects. By selectively manipulating the nature of interactions between protein molecules, we determined that excluded volume effects induce sub-diffusive dynamics at sub-microsecond timescales. These findings may help to explain the diffusion-mediated effects of protein crowding on cellular processes.
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Affiliation(s)
- Vijay Phanindra Srikanth Kompella
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin Institute for Data Science, Curtin University, Perth, Western Australia, Australia; Department of Physics, Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, United Kingdom
| | - Maria Carmen Romano
- Department of Physics, Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, United Kingdom; Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Ian Stansfield
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Ricardo L Mancera
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin Institute for Data Science, Curtin University, Perth, Western Australia, Australia.
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9
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Ota C, Konishi T, Tanaka SI, Takano K. Induced Circular Dichroism Analysis of Thermally Induced Conformational Changes on Protein Binding Sites Under a Crowding Environment. Chemphyschem 2024; 25:e202300593. [PMID: 37845184 DOI: 10.1002/cphc.202300593] [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: 08/20/2023] [Revised: 10/15/2023] [Accepted: 10/16/2023] [Indexed: 10/18/2023]
Abstract
Protein-ligand interactions in crowded cellular environments play a crucial role in biological functions. The crowded environment can perturb the overall protein structure and local conformation, thereby influencing the binding pathway of protein-ligand reactions within the cellular milieu. Therefore, a detailed understanding of the local conformation is crucial for elucidating the intricacies of protein-ligand interactions in crowded cellular environments. In this study, we investigated the feasibility of induced circular dichroism (ICD) using 8-anilinonaphthalene-1-sulfonic acid (ANS) for local conformational analysis at the binding site in a crowding environment. Bovine serum albumin (BSA) concentration-dependent measurements were performed to assess the feasibility of ANS-ICD for analyzing protein interior binding sites. The results showed distinct changes in the ANS-ICD spectra of BSA solutions, indicating their potential for analyzing the internal conformation of proteins. Moreover, temperature-dependent measurements were performed in dilute and crowding environments, revealing distinct denaturation pathways of BSA binding sites. Principal component analysis of ANS-ICD spectral changes revealed lower temperature pre-denaturation in the crowded solution than that in the diluted solution, suggesting destabilization of binding sites owing to self-crowding repulsive interactions. The established ANS-ICD method can provide valuable conformational insights into protein-ligand interactions in crowded cellular environments.
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Affiliation(s)
- Chikashi Ota
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Tomoya Konishi
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Sakyo-ku, Kyoto, 606-8522, Japan
| | - Shun-Ichi Tanaka
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Sakyo-ku, Kyoto, 606-8522, Japan
| | - Kazufumi Takano
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Sakyo-ku, Kyoto, 606-8522, Japan
- Kazufumi Takano - Department of Biomolecular Chemistry, Kyoto Prefectural University, Sakyo-ku, Kyoto, 606-8522, Japan
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10
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Lorenz-Ochoa KA, Baiz CR. Ultrafast Spectroscopy Reveals Slow Water Dynamics in Biocondensates. J Am Chem Soc 2023; 145:27800-27809. [PMID: 38061016 DOI: 10.1021/jacs.3c10862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Cells achieve high spatiotemporal control over biochemical processes through compartmentalization to membrane-bound as well as membraneless organelles that assemble by liquid-liquid phase separation. Characterizing the balance of forces within these environments is essential to understanding their stability and function, and water is an integral part of the condensate, playing an important role in mediating electrostatic and hydrogen-bonding interactions. Here, we investigate the ultrafast, picosecond hydrogen-bond dynamics of a model biocondensate consisting of a peptide poly-l-arginine (Poly-R) and the nucleic acid adenosine monophosphate (AMP) using coherent two-dimensional infrared (2D IR) spectroscopy. We investigated three vibrational modes: the arginine side-chain C═N stretches, an AMP ring mode, and the amide backbone carbonyl stretching modes. Dynamics slow considerably between the dilute phase and the condensate phase for each vibrational probe. For example, the arginine side-chain C═N modes slow from 0.38 to 2.26 ps due to strong electrostatic interactions. All-atom molecular dynamics simulations provide an atomistic interpretation of the H-bond network disruption resulting from electrostatic contributions as well as collapse within the condensate. Simulations predict that a fraction of water molecules are highly constrained within the condensate, explaining the observed slowdown in the H-bond dynamics.
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Affiliation(s)
- Keegan A Lorenz-Ochoa
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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11
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Seitz C, Deveci İ, McCammon JA. Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics. J Phys Chem Lett 2023; 14:9926-9934. [PMID: 37903229 PMCID: PMC10641874 DOI: 10.1021/acs.jpclett.3c02524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/01/2023]
Abstract
All protein simulations are conducted with varying degrees of simplification, oftentimes with unknown ramifications about how these simplifications affect the interpretability of the results. In this work, we investigated how protein glycosylation and lateral crowding effects modulate an array of properties characterizing the stability and dynamics of influenza neuraminidase. We constructed three systems: (1) glycosylated neuraminidase in a whole virion (i.e., crowded membrane) environment, (2) glycosylated neuraminidase in its own lipid bilayer, and (3) unglycosylated neuraminidase in its own lipid bilayer. We saw that glycans tend to stabilize the protein structure and reduce its conformational flexibility while restricting the solvent movement. Conversely, a crowded membrane environment encouraged exploration of the free energy landscape and a large-scale conformational change, while making the protein structure more compact. Understanding these effects informs what factors one must consider in attempting to recapture the desired level of physical accuracy.
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Affiliation(s)
- Christian Seitz
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - İlker Deveci
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - J. Andrew McCammon
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
- Department
of Pharmacology, University of California,
San Diego, La Jolla, California 92093, United States
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12
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Borges-Araújo L, Patmanidis I, Singh AP, Santos LHS, Sieradzan AK, Vanni S, Czaplewski C, Pantano S, Shinoda W, Monticelli L, Liwo A, Marrink SJ, Souza PCT. Pragmatic Coarse-Graining of Proteins: Models and Applications. J Chem Theory Comput 2023; 19:7112-7135. [PMID: 37788237 DOI: 10.1021/acs.jctc.3c00733] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The molecular details involved in the folding, dynamics, organization, and interaction of proteins with other molecules are often difficult to assess by experimental techniques. Consequently, computational models play an ever-increasing role in the field. However, biological processes involving large-scale protein assemblies or long time scale dynamics are still computationally expensive to study in atomistic detail. For these applications, employing coarse-grained (CG) modeling approaches has become a key strategy. In this Review, we provide an overview of what we call pragmatic CG protein models, which are strategies combining, at least in part, a physics-based implementation and a top-down experimental approach to their parametrization. In particular, we focus on CG models in which most protein residues are represented by at least two beads, allowing these models to retain some degree of chemical specificity. A description of the main modern pragmatic protein CG models is provided, including a review of the most recent applications and an outlook on future perspectives in the field.
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Affiliation(s)
- Luís Borges-Araújo
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
| | - Ilias Patmanidis
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Akhil P Singh
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
| | - Lucianna H S Santos
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur, Inserm, CNRS, 06560 Valbonne, France
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Wataru Shinoda
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita, Okayama 700-8530, Japan
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
| | - Adam Liwo
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
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13
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Kolesnikov ES, Gushchin IY, Zhilyaev PA, Onufriev AV. Why Na+ has higher propensity than K+ to condense DNA in a crowded environment. J Chem Phys 2023; 159:145103. [PMID: 37815107 DOI: 10.1063/5.0159341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/22/2023] [Indexed: 10/11/2023] Open
Abstract
Experimentally, in the presence of the crowding agent polyethylene glycol (PEG), sodium ions compact double-stranded DNA more readily than potassium ions. Here, we have used molecular dynamics simulations and the "ion binding shells model" of DNA condensation to provide an explanation for the observed variations in condensation of short DNA duplexes in solutions containing different monovalent cations and PEG; several predictions are made. According to the model we use, externally bound ions contribute the most to the ion-induced aggregation of DNA duplexes. The simulations reveal that for two adjacent DNA duplexes, the number of externally bound Na+ ions is larger than the number of K+ ions over a wide range of chloride concentrations in the presence of PEG, providing a qualitative explanation for the higher propensity of sodium ions to compact DNA under crowded conditions. The qualitative picture is confirmed by an estimate of the corresponding free energy of DNA aggregation that is at least 0.2kBT per base pair more favorable in solution with NaCl than with KCl at the same ion concentration. The estimated attraction free energy of DNA duplexes in the presence of Na+ depends noticeably on the DNA sequence; we predict that AT-rich DNA duplexes are more readily condensed than GC-rich ones in the presence of Na+. Counter-intuitively, the addition of a small amount of a crowding agent with high affinity for the specific condensing ion may lead to the weakening of the ion-mediated DNA-DNA attraction, shifting the equilibrium away from the DNA condensed phase.
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Affiliation(s)
- Egor S Kolesnikov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Department of Physics, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Ivan Yu Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Petr A Zhilyaev
- The Center for Materials Technologies, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, Moscow 121205, Russia
| | - Alexey V Onufriev
- Department of Physics, Virginia Tech, Blacksburg, Virginia 24061, USA
- Department of Computer Science, Virginia Tech, 2160C Torgersen Hall, Blacksburg, Virginia 24061, USA
- Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, USA
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14
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Seitz C, Deveci İ, McCammon JA. Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.10.556910. [PMID: 37745347 PMCID: PMC10515755 DOI: 10.1101/2023.09.10.556910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
All protein simulations are conducted with varying degrees of simplifications, oftentimes with unknown ramifications on how these simplifications affect the interpretability of the results. In this work we investigated how protein glycosylation and lateral crowding effects modulate an array of properties characterizing the stability and dynamics of influenza neuraminidase. We constructed three systems: 1) Glycosylated neuraminidase in a whole virion (i.e. crowded membrane) environment 2) Glycosylated neuraminidase in its own lipid bilayer 3) Unglycosylated neuraminidase in its own lipid bilayer. We saw that glycans tend to stabilize the protein structure and reduce its conformational flexibility while restricting solvent movement. Conversely, a crowded membrane environment encouraged exploration of the free energy landscape and a large scale conformational change while making the protein structure more compact. Understanding these effects informs what factors one must consider while attempting to recapture the desired level of physical accuracy.
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Affiliation(s)
- Christian Seitz
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - İlker Deveci
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
- Department of Pharmacology, University of California, San Diego, La Jolla, California
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15
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Słyk E, Skóra T, Kondrat S. Minimal Coarse-Grained Model for Immunoglobulin G: Diffusion and Binding under Crowding. J Phys Chem B 2023; 127:7442-7448. [PMID: 37591305 PMCID: PMC10476189 DOI: 10.1021/acs.jpcb.3c02383] [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: 04/10/2023] [Revised: 07/25/2023] [Indexed: 08/19/2023]
Abstract
Immunoglobulin G (IgG) is the most common type of antibody found in blood and extracellular fluids and plays an essential role in our immune response. However, studies of the dynamics and reaction kinetics of IgG-antigen binding under physiological crowding conditions are scarce. Herein, we develop a coarse-grained model of IgG consisting of only six beads that we find minimal for a coarse representation of IgG's shape and a decent reproduction of its flexibility and diffusion properties measured experimentally. Using this model in Brownian dynamics simulations, we find that macromolecular crowding affects only slightly the IgG's flexibility, as described by the distribution of angles between the IgG's arms and stem. Our simulations indicate that, contrary to expectations, crowders slow down the translational diffusion of an IgG less strongly than they do for a smaller Ficoll 70, which we relate to the IgG's conformational size changes induced by crowding. We also find that crowders affect the binding kinetics by decreasing the rate of the first binding step and enhancing the second binding step.
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Affiliation(s)
- Edyta Słyk
- Institute
of Physical Chemistry, Polish Academy of
Sciences, Warsaw 01-224, Poland
- Department
of Theoretical Chemistry, Institute of Chemical Sciences, Faculty
of Chemistry, Maria Curie-Skłodowska
University in Lublin, Lublin 20-031, Poland
| | - Tomasz Skóra
- Institute
of Physical Chemistry, Polish Academy of
Sciences, Warsaw 01-224, Poland
| | - Svyatoslav Kondrat
- Institute
of Physical Chemistry, Polish Academy of
Sciences, Warsaw 01-224, Poland
- Institute
for Computational Physics, University of
Stuttgart, Stuttgart 70569, Germany
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16
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Dandekar BR, Majumdar BB, Mondal J. Nonmonotonic Modulation of the Protein-Ligand Recognition Event by Inert Crowders. J Phys Chem B 2023; 127:7449-7461. [PMID: 37590118 DOI: 10.1021/acs.jpcb.3c03946] [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: 08/19/2023]
Abstract
The ubiquitous event of a protein recognizing small molecules or ligands at its native binding site is crucial for initiating major biological processes. However, how a crowded environment, as is typically represented by a cellular interior, would modulate the protein-ligand search process is largely debated. Excluded volume-based theory suggests that the presence of an inert crowder would reinforce a steady stabilization and enhancement of the protein-ligand recognition process. Here, we counter this long-held perspective via the molecular dynamics simulation and Markov state model of the protein-ligand recognition event in the presence of inert crowders. Specifically, we demonstrate that, depending on concentration, even purely inert crowders can exert a nonmonotonic effect via either stabilizing or destabilizing the protein-ligand binding event. Analysis of the kinetic network of binding pathways reveals that the crowders would either modulate precedent non-native on-pathway intermediates or would devise additional ones in a multistate recognition event across a wide range of concentrations. As an important insight, crowders gradually shift the relative transitional preference of these intermediates toward a native-bound state, with ligand residence time at the binding pocket dictating the trend of nonmonotonic concentration dependence by simple inert crowders.
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17
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Boyuklieva R, Zagorchev P, Pilicheva B. Computational, In Vitro, and In Vivo Models for Nose-to-Brain Drug Delivery Studies. Biomedicines 2023; 11:2198. [PMID: 37626694 PMCID: PMC10452071 DOI: 10.3390/biomedicines11082198] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/27/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
Direct nose-to-brain drug delivery offers the opportunity to treat central nervous system disorders more effectively due to the possibility of drug molecules reaching the brain without passing through the blood-brain barrier. Such a delivery route allows the desired anatomic site to be reached while ensuring drug effectiveness, minimizing side effects, and limiting drug losses and degradation. However, the absorption of intranasally administered entities is a complex process that considerably depends on the interplay between the characteristics of the drug delivery systems and the nasal mucosa. Various preclinical models (in silico, in vitro, ex vivo, and in vivo) are used to study the transport of drugs after intranasal administration. The present review article attempts to summarize the different computational and experimental models used so far to investigate the direct delivery of therapeutic agents or colloidal carriers from the nasal cavity to the brain tissue. Moreover, it provides a critical evaluation of the data available from different studies and identifies the advantages and disadvantages of each model.
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Affiliation(s)
- Radka Boyuklieva
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria;
- Research Institute, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria;
| | - Plamen Zagorchev
- Research Institute, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria;
- Department of Medical Physics and Biophysics, Faculty of Pharmacy, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria
| | - Bissera Pilicheva
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria;
- Research Institute, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria;
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18
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Malik MZ, Dashti M, Fatima Y, Channanath A, John SE, Singh RKB, Al-Mulla F, Thanaraj TA. Disruption in the regulation of casein kinase 2 in circadian rhythm leads to pathological states: cancer, diabetes and neurodegenerative disorders. Front Mol Neurosci 2023; 16:1217992. [PMID: 37475884 PMCID: PMC10354274 DOI: 10.3389/fnmol.2023.1217992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/12/2023] [Indexed: 07/22/2023] Open
Abstract
Introduction Circadian rhythm maintains the sleep-wake cycle in biological systems. Various biological activities are regulated and modulated by the circadian rhythm, disruption of which can result in onset of diseases. Robust rhythms of phosphorylation profiles and abundances of PERIOD (PER) proteins are thought to be the master keys that drive circadian clock functions. The role of casein kinase 2 (CK2) in circadian rhythm via its direct interactions with the PER protein has been extensively studied; however, the exact mechanism by which it affects circadian rhythms at the molecular level is not known. Methods Here, we propose an extended circadian rhythm model in Drosophila that incorporates the crosstalk between the PER protein and CK2. We studied the regulatory role of CK2 in the dynamics of PER proteins involved in circadian rhythm using the stochastic simulation algorithm. Results We observed that variations in the concentration of CK2 in the circadian rhythm model modulates the PER protein dynamics at different cellular states, namely, active, weakly active, and rhythmic death. These oscillatory states may correspond to distinct pathological cellular states of the living system. We find molecular noise at the expression level of CK2 to switch normal circadian rhythm to any of the three above-mentioned circadian oscillatory states. Our results suggest that the concentration levels of CK2 in the system has a strong impact on its dynamics, which is reflected in the time evolution of PER protein. Discussion We believe that our findings can contribute towards understanding the molecular mechanisms of circadian dysregulation in pathways driven by the PER mutant genes and their pathological states, including cancer, obesity, diabetes, neurodegenerative disorders, and socio-psychological disease.
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Affiliation(s)
- Md. Zubbair Malik
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Mohammed Dashti
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Yasmin Fatima
- Department of Computational Biology and Bioinformatics, Sam Higginbottom Institute of Agriculture, Technology and Sciences (Formerly Allahabad Agricultural Institute-Deemed University), Allahabad, India
| | - Arshad Channanath
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Sumi Elsa John
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - R. K. Brojen Singh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
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19
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Skóra T, Janssen M, Carlson A, Kondrat S. Crowding-Regulated Binding of Divalent Biomolecules. PHYSICAL REVIEW LETTERS 2023; 130:258401. [PMID: 37418731 DOI: 10.1103/physrevlett.130.258401] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 05/08/2023] [Indexed: 07/09/2023]
Abstract
Macromolecular crowding affects biophysical processes as diverse as diffusion, gene expression, cell growth, and senescence. Yet, there is no comprehensive understanding of how crowding affects reactions, particularly multivalent binding. Herein, we use scaled particle theory and develop a molecular simulation method to investigate the binding of monovalent to divalent biomolecules. We find that crowding can increase or reduce cooperativity-the extent to which the binding of a second molecule is enhanced after binding a first molecule-by orders of magnitude, depending on the sizes of the involved molecular complexes. Cooperativity generally increases when a divalent molecule swells and then shrinks upon binding two ligands. Our calculations also reveal that, in some cases, crowding enables binding that does not occur otherwise. As an immunological example, we consider immunoglobulin G-antigen binding and show that crowding enhances its cooperativity in bulk but reduces it when an immunoglobulin G binds antigens on a surface.
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Affiliation(s)
- Tomasz Skóra
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Mathijs Janssen
- Department of Mathematics, Mechanics Division, University of Oslo, N-0851 Oslo, Norway
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Montebello, N-0379 Oslo, Norway
- Norwegian University of Life Sciences, Faculty of Science and Technology, Pb 5003, 1433 Ås, Norway
| | - Andreas Carlson
- Department of Mathematics, Mechanics Division, University of Oslo, N-0851 Oslo, Norway
| | - Svyatoslav Kondrat
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
- Institute for Computational Physics, University of Stuttgart, Stuttgart 70569, Germany
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20
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Shew CY, Yoshikawa K. Crowding effect on the alignment of rod molecules confined in a spherical cavity. Chem Phys Lett 2023. [DOI: 10.1016/j.cplett.2023.140437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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21
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Ostrowska N, Feig M, Trylska J. Varying molecular interactions explain aspects of crowder-dependent enzyme function of a viral protease. PLoS Comput Biol 2023; 19:e1011054. [PMID: 37098073 PMCID: PMC10162569 DOI: 10.1371/journal.pcbi.1011054] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 05/05/2023] [Accepted: 03/28/2023] [Indexed: 04/26/2023] Open
Abstract
Biochemical processes in cells, including enzyme-catalyzed reactions, occur in crowded conditions with various background macromolecules occupying up to 40% of cytoplasm's volume. Viral enzymes in the host cell also encounter such crowded conditions as they often function at the endoplasmic reticulum membranes. We focus on an enzyme encoded by the hepatitis C virus, the NS3/4A protease, which is crucial for viral replication. We have previously found experimentally that synthetic crowders, polyethylene glycol (PEG) and branched polysucrose (Ficoll), differently affect the kinetic parameters of peptide hydrolysis catalyzed by NS3/4A. To gain understanding of the reasons for such behavior, we perform atomistic molecular dynamics simulations of NS3/4A in the presence of either PEG or Ficoll crowders and with and without the peptide substrates. We find that both crowder types make nanosecond long contacts with the protease and slow down its diffusion. However, they also affect the enzyme structural dynamics; crowders induce functionally relevant helical structures in the disordered parts of the protease cofactor, NS4A, with the PEG effect being more pronounced. Overall, PEG interactions with NS3/4A are slightly stronger but Ficoll forms more hydrogen bonds with NS3. The crowders also interact with substrates; we find that the substrate diffusion is reduced much more in the presence of PEG than Ficoll. However, contrary to NS3, the substrate interacts more strongly with Ficoll than with PEG crowders, with the substrate diffusion being similar to crowder diffusion. Importantly, crowders also affect the substrate-enzyme interactions. We observe that both PEG and Ficoll enhance the presence of substrates near the active site, especially near catalytic H57 but Ficoll crowders increase substrate binding more than PEG molecules.
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Affiliation(s)
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
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22
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Pradhan S, Rath R, Biswas M. GB1 Dimerization in Crowders: A Multiple Resolution Approach. J Chem Inf Model 2023; 63:1570-1577. [PMID: 36858485 DOI: 10.1021/acs.jcim.3c00012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
In-cell protein-protein association, which is crucial in enzyme catalysis and polymerization, occurs in an environment that is highly heterogeneous and crowded. The crowder molecules exclude the reactant molecules from occupying certain regions of the cell, resulting in changes in the reaction thermodynamics and kinetics. Recent studies, both experiment and simulations, revealed that the nature of the interaction between crowder and protein species, in particular the soft interactions, plays an important role in crowder induced effects on protein association. To this end, from a simulation perspective, it is important to decipher the level of structural resolution in a protein-crowder model that can faithfully capture the influence of crowding on protein association. Here, we investigate the dimerization of model system GB1 in the presence of lysozyme crowders at two structural resolutions. The lower resolution model assumes both protein and crowder species as spherical beads, similar to the analytical scaled particle theory model, whereas the higher resolution model retains residue specific structural details for protein and crowder species. From the higher resolution model, it is found that GB1 dimer formation is destabilized in the presence of lysozyme crowders, and the destabilization is more for the side-by-side dimer compared to the domain-swapped dimer, in qualitative agreement with experimental findings. However, the low resolution CG model predicts stabilization of the dimers in the presence of the lysozyme crowder, similar to the SPT model. Our results indicate a nontrivial role of the choice of model resolution in computer simulation studies investigating crowder induced effects.
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Affiliation(s)
- Sweta Pradhan
- National Institute of Technology Rourkela, Rourkela 769008, India
| | - Rajendra Rath
- National Institute of Technology Rourkela, Rourkela 769008, India
| | - Mithun Biswas
- National Institute of Technology Rourkela, Rourkela 769008, India
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23
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Panigrahy S, Sahu R, Reddy SK, Nayar D. Structure, energetics and dynamics in crowded amino acid solutions: a molecular dynamics study. Phys Chem Chem Phys 2023; 25:5430-5442. [PMID: 36744506 DOI: 10.1039/d2cp04238j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A comprehensive understanding of crowding effects on biomolecular processes necessitates investigating the bulk thermodynamic and kinetic properties of the solutions with an accurate molecular representation of the crowded milieu. Recent studies have reparameterized the non-bonded dispersion interaction of solutes to precisely model intermolecular interactions, which would circumvent artificial aggregation as shown by the original force-fields. However, the performance of this reparameterization is yet to be assessed for concentrated crowded solutions in terms of investigating the hydration shell structure, energetics and dynamics. In this study, we perform molecular dynamics simulations of crowded aqueous solutions of five zwitterionic neutral amino acids (Gly, Ala, Thr, Pro, and Ser), mimicking the molecular crowding environment, using a modified AMBER ff99SB-ILDN force-field. We systematically examine and show that the reproducibility of the osmotic coefficients, density, viscosity and self-diffusivity of amino acids improves using the modified force-field in crowded concentrations. The modified force-field also improves the structuring of the solute solvation shells, solute interaction energy and convergence of tails of radial distribution functions, indicating reduction in the artificial aggregation. Our results also indicate that the hydrogen bonding network of water weakens and water molecules anomalously diffuse at small time scales in the crowded solutions. These results underscore the significance of examining the solution properties and anomalous hydration behaviour of water in crowded solutions, which have implications in shaping the structure and dynamics of biomolecules. The findings also illustrate the improvement in predicting bulk solution properties using the modified force-field, thereby providing an approach towards accurate modeling of crowded molecular solutions.
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Affiliation(s)
- Sibasankar Panigrahy
- Department of Materials Science and Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India.
| | - Rahul Sahu
- Center for Computational and Data Sciences, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Sandeep K Reddy
- Center for Computational and Data Sciences, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Divya Nayar
- Department of Materials Science and Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India.
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24
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Macromolecular Crowding Is Surprisingly Unable to Deform the Structure of a Model Biomolecular Condensate. BIOLOGY 2023; 12:biology12020181. [PMID: 36829460 PMCID: PMC9952705 DOI: 10.3390/biology12020181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/27/2023]
Abstract
The crowded interior of a living cell makes performing experiments on simpler in vitro systems attractive. Although these reveal interesting phenomena, their biological relevance can be questionable. A topical example is the phase separation of intrinsically disordered proteins into biomolecular condensates, which is proposed to underlie the membrane-less compartmentalization of many cellular functions. How a cell reliably controls biochemical reactions in compartments open to the compositionally-varying cytoplasm is an important question for understanding cellular homeostasis. Computer simulations are often used to study the phase behavior of model biomolecular condensates, but the number of relevant parameters increases as the number of protein components increases. It is unfeasible to exhaustively simulate such models for all parameter combinations, although interesting phenomena are almost certainly hidden in their high-dimensional parameter space. Here, we have studied the phase behavior of a model biomolecular condensate in the presence of a polymeric crowding agent. We used a novel compute framework to execute dozens of simultaneous simulations spanning the protein/crowder concentration space. We then combined the results into a graphical representation for human interpretation, which provided an efficient way to search the model's high-dimensional parameter space. We found that steric repulsion from the crowder drives a near-critical system across the phase boundary, but the molecular arrangement within the resulting biomolecular condensate is rather insensitive to the crowder concentration and molecular weight. We propose that a cell may use the local cytoplasmic concentration to assist the formation of biomolecular condensates, while relying on the dense phase to reliably provide a stable, structured, fluid milieu for cellular biochemistry despite being open to its changing environment.
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25
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Sarkar D, Kulke M, Vermaas JV. LongBondEliminator: A Molecular Simulation Tool to Remove Ring Penetrations in Biomolecular Simulation Systems. Biomolecules 2023; 13:biom13010107. [PMID: 36671493 PMCID: PMC9856086 DOI: 10.3390/biom13010107] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/30/2022] [Accepted: 01/01/2023] [Indexed: 01/07/2023] Open
Abstract
We develop a workflow, implemented as a plugin to the molecular visualization program VMD, that can fix ring penetrations with minimal user input. LongBondEliminator, detects ring piercing artifacts by the long, strained bonds that are the local minimum energy conformation during minimization for some assembled simulation system. The LongBondEliminator tool then automatically treats regions near these long bonds using multiple biases applied through NAMD. By combining biases implemented through the collective variables module, density-based forces, and alchemical techniques in NAMD, LongBondEliminator will iteratively alleviate long bonds found within molecular simulation systems. Through three concrete examples with increasing complexity, a lignin polymer, an viral capsid assembly, and a large, highly glycosylated protein aggrecan, we demonstrate the utility for this method in eliminating ring penetrations from classical MD simulation systems. The tool is available via gitlab as a VMD plugin, and has been developed to be generically useful across a variety of biomolecular simulations.
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26
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Sanjeev BS, Chitara D, Madhumalar A. Physiological models to study the effect of molecular crowding on multi-drug bound proteins: insights from SARS-CoV-2 main protease. J Biomol Struct Dyn 2022; 40:13564-13580. [PMID: 34699337 DOI: 10.1080/07391102.2021.1993342] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Molecular Dynamics simulations are often used in drug design. However, such simulations do not account for the physiological environment of the receptor; hence overlook its impact on biomolecular interactions. To address this lacuna, we identified three objectives to pursue - develop models of physiological environment, study a drug-receptor complex in such environments, and identify methods to analyze these complicated simulations. Two novel physiological models were developed and studied. The first, called 'm10', comprises of 10 of the most abundant cytoplasmic metabolites at physiological concentrations. The second, called 'phy', supplements m10 with an additional crowder protein to elicit macromolecular crowding effect. The main protease (Mpro) of SARS-CoV-2, being essential for viral replication, is an attractive drug target for COVID-19. Hence, we chose Mpro docked with multiple drugs as our model drug-receptor system. With a plethora of compounds, physiological systems can be exceedingly large and complex. A novel Spark-based software (SparkTraj) was developed to rapidly analyze non-specific contacts and water interactions. Our study shows that crowding enhances the difference in the dynamics of apo- vs drug-bound complexes. Metabolites, at times as a cluster, were seen interacting with the protease, drugs, and binding sites in drug-free receptor. Except one that crawled to an adjacent pocket in phy, the drugs remained in their respective pockets in all simulations. Given these observations, we hope that the models and approach presented here would help the optimization, evaluation, and selection of potential drugs. Generic biomolecular dynamics could also benefit from such models and tools.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- B S Sanjeev
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, India
| | - Dheeraj Chitara
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, India
| | - Arumugam Madhumalar
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi, India
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27
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Rodriguez Barroso LG, Azaman FA, Pogue R, Devine D, Fournet MB. Monitoring In Vitro Extracellular Matrix Protein Conformations in the Presence of Biomimetic Bone-Regeneration Scaffolds Using Functionalized Gold-Edge-Coated Triangular Silver Nanoparticles. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 13:57. [PMID: 36615967 PMCID: PMC9823344 DOI: 10.3390/nano13010057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
In the cellular environment, high noise levels, such as fluctuations in biochemical reactions, protein variability, molecular diffusion, cell-to-cell contact, and pH, can both mediate and interfere with cellular functions. In this work, gold edge-coated triangular silver nanoparticles (AuTSNP) were validated as a promising new tool to indicate protein conformational transitions in cultured cells and to monitor essential protein activity in the presence of an optimized bone biomimetic chitosan-based scaffold whose rational design mimics the ECM as a natural scaffold. A chitosan-based scaffold formulation with hydroxyapatite (CS/HAp) was selected due to its promising features for orthopedic applications, including combined high mechanical strength biocompatibility and biodegradability. Functionalized AuTSNP-based tests with the model ECM protein, fibronectin (Fn), illustrate that the protein interactions can be clearly sensed over time through the local surface plasmon resonance (LSPR) technique. This demonstrates that AuTNSP are a powerful tool to detect protein conformational activity in the presence of biomimetic bone tissue regeneration scaffolds within a cellular environment that comprises a diversity of molecular cues.
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Affiliation(s)
- Laura G. Rodriguez Barroso
- Technological University of the Shannon: Midlands Midwest, Dublin Rd., N37 HD68 Athlone, Co. Westmeath, Ireland
| | - Farah Alwani Azaman
- Technological University of the Shannon: Midlands Midwest, Dublin Rd., N37 HD68 Athlone, Co. Westmeath, Ireland
| | - Robert Pogue
- Technological University of the Shannon: Midlands Midwest, Dublin Rd., N37 HD68 Athlone, Co. Westmeath, Ireland
- Universidade Católica de Brasília, Campus Asa Norte. SGAN Módulo B 916 Avenida W5—Asa Norte, Brasilia 70790-160-DF, Brazil
| | - Declan Devine
- Technological University of the Shannon: Midlands Midwest, Dublin Rd., N37 HD68 Athlone, Co. Westmeath, Ireland
| | - Margaret Brennan Fournet
- Technological University of the Shannon: Midlands Midwest, Dublin Rd., N37 HD68 Athlone, Co. Westmeath, Ireland
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28
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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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29
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Jenkins NW, Kundrotas PJ, Vakser IA. Size of the protein-protein energy funnel in crowded environment. Front Mol Biosci 2022; 9:1031225. [PMID: 36425657 PMCID: PMC9679368 DOI: 10.3389/fmolb.2022.1031225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022] Open
Abstract
Association of proteins to a significant extent is determined by their geometric complementarity. Large-scale recognition factors, which directly relate to the funnel-like intermolecular energy landscape, provide important insights into the basic rules of protein recognition. Previously, we showed that simple energy functions and coarse-grained models reveal major characteristics of the energy landscape. As new computational approaches increasingly address structural modeling of a whole cell at the molecular level, it becomes important to account for the crowded environment inside the cell. The crowded environment drastically changes protein recognition properties, and thus significantly alters the underlying energy landscape. In this study, we addressed the effect of crowding on the protein binding funnel, focusing on the size of the funnel. As crowders occupy the funnel volume, they make it less accessible to the ligands. Thus, the funnel size, which can be defined by ligand occupancy, is generally reduced with the increase of the crowders concentration. This study quantifies this reduction for different concentration of crowders and correlates this dependence with the structural details of the interacting proteins. The results provide a better understanding of the rules of protein association in the crowded environment.
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Affiliation(s)
- Nathan W. Jenkins
- Computational Biology Program, The University of Kansas, Lawrence, KS, United States
| | - Petras J. Kundrotas
- Computational Biology Program, The University of Kansas, Lawrence, KS, United States
- *Correspondence: Petras J. Kundrotas, ; Ilya A. Vakser,
| | - Ilya A. Vakser
- Computational Biology Program, The University of Kansas, Lawrence, KS, United States
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, United States
- *Correspondence: Petras J. Kundrotas, ; Ilya A. Vakser,
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30
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Kulke M, Vermaas JV. Reversible Unwrapping Algorithm for Constant-Pressure Molecular Dynamics Simulations. J Chem Theory Comput 2022; 18:6161-6171. [PMID: 36129782 DOI: 10.1021/acs.jctc.2c00327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular simulation technologies have afforded researchers a unique look into the nanoscale interactions driving physical processes. However, a limitation for molecular dynamics (MD) simulations is that they must be performed on finite-sized systems in order to map onto computational resources. To minimize artifacts arising from finite-sized simulation systems, it is common practice for MD simulations to be performed with periodic boundary conditions (PBCs). However, in order to calculate specific physical properties, such as mean square displacements to calculate diffusion coefficients, continuous particle trajectories where the atomic movements are continuous and do not jump between cell faces are required. In these cases, modifying atomic coordinates through unwrapping schemes is an essential post-processing tool to remove these jumps. Here, two established trajectory unwrapping schemes are applied to 1 μs wrapped trajectories for a small water box and lysozyme in water. The existing schemes can result in spurious diffusion coefficients, long bonds within unwrapped molecules, and inconsistent atomic coordinates when coordinates are rewrapped after unwrapping. We determine that prior unwrapping schemes do not account for changing periodic box dimensions and introduce an additional correction term to the existing displacement unwrapping scheme to correct for these artifacts. We also demonstrate that the resulting algorithm is a hybrid between the existing heuristic and displacement unwrapping schemes. After treatment using this new unwrapping scheme, molecular geometries are correct even after long simulations. In anticipation for longer MD trajectories, we develop implementations for this new scheme in multiple PBC handling tools.
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Affiliation(s)
- Martin Kulke
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, 612 Wilson Rd, East Lansing, Michigan 48824, United States
| | - Josh V Vermaas
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, 612 Wilson Rd, East Lansing, Michigan 48824, United States
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31
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Beck C, Grimaldo M, Lopez H, Da Vela S, Sohmen B, Zhang F, Oettel M, Barrat JL, Roosen-Runge F, Schreiber F, Seydel T. Short-Time Transport Properties of Bidisperse Suspensions of Immunoglobulins and Serum Albumins Consistent with a Colloid Physics Picture. J Phys Chem B 2022; 126:7400-7408. [PMID: 36112146 PMCID: PMC9527755 DOI: 10.1021/acs.jpcb.2c02380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The crowded environment of biological systems such as
the interior
of living cells is occupied by macromolecules with a broad size distribution.
This situation of polydispersity might influence the dependence of
the diffusive dynamics of a given tracer macromolecule in a monodisperse
solution on its hydrodynamic size and on the volume fraction. The
resulting size dependence of diffusive transport crucially influences
the function of a living cell. Here, we investigate a simplified model
system consisting of two constituents in aqueous solution, namely,
of the proteins bovine serum albumin (BSA) and bovine polyclonal gamma-globulin
(Ig), systematically depending on the total volume fraction and ratio
of these constituents. From high-resolution quasi-elastic neutron
spectroscopy, the separate apparent short-time diffusion coefficients
for BSA and Ig in the mixture are extracted, which show substantial
deviations from the diffusion coefficients measured in monodisperse
solutions at the same total volume fraction. These deviations can
be modeled quantitatively using results from the short-time rotational
and translational diffusion in a two-component hard sphere system
with two distinct, effective hydrodynamic radii. Thus, we find that
a simple colloid picture well describes short-time diffusion in binary
mixtures as a function of the mixing ratio and the total volume fraction.
Notably, the self-diffusion of the smaller protein BSA in the mixture
is faster than the diffusion in a pure BSA solution, whereas the self-diffusion
of Ig in the mixture is slower than in the pure Ig solution.
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Affiliation(s)
- Christian Beck
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
- Institut Max von Laue─Paul Langevin (ILL), CS 20156, F-38042 Grenoble Cedex 9, France
| | - Marco Grimaldo
- Institut Max von Laue─Paul Langevin (ILL), CS 20156, F-38042 Grenoble Cedex 9, France
| | - Hender Lopez
- School of Physics and Optometric & Clinical Sciences, Technological University Dublin, D07 XT95 Grangegorman, Ireland
| | - Stefano Da Vela
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Benedikt Sohmen
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Martin Oettel
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | | | - Felix Roosen-Runge
- Department of Biomedical Science and Biofilms-Research Center for Biointerfaces (BRCB), Malmö University, 20506 Malmö, Sweden
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Tilo Seydel
- Institut Max von Laue─Paul Langevin (ILL), CS 20156, F-38042 Grenoble Cedex 9, France
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32
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Matsubara D, Kasahara K, Dokainish HM, Oshima H, Sugita Y. Modified Protein-Water Interactions in CHARMM36m for Thermodynamics and Kinetics of Proteins in Dilute and Crowded Solutions. Molecules 2022; 27:molecules27175726. [PMID: 36080494 PMCID: PMC9457699 DOI: 10.3390/molecules27175726] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/30/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Proper balance between protein-protein and protein-water interactions is vital for atomistic molecular dynamics (MD) simulations of globular proteins as well as intrinsically disordered proteins (IDPs). The overestimation of protein-protein interactions tends to make IDPs more compact than those in experiments. Likewise, multiple proteins in crowded solutions are aggregated with each other too strongly. To optimize the balance, Lennard-Jones (LJ) interactions between protein and water are often increased about 10% (with a scaling parameter, λ = 1.1) from the existing force fields. Here, we explore the optimal scaling parameter of protein-water LJ interactions for CHARMM36m in conjunction with the modified TIP3P water model, by performing enhanced sampling MD simulations of several peptides in dilute solutions and conventional MD simulations of globular proteins in dilute and crowded solutions. In our simulations, 10% increase of protein-water LJ interaction for the CHARMM36m cannot maintain stability of a small helical peptide, (AAQAA)3 in a dilute solution and only a small modification of protein-water LJ interaction up to the 3% increase (λ = 1.03) is allowed. The modified protein-water interactions are applicable to other peptides and globular proteins in dilute solutions without changing thermodynamic properties from the original CHARMM36m. However, it has a great impact on the diffusive properties of proteins in crowded solutions, avoiding the formation of too sticky protein-protein interactions.
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Affiliation(s)
- Daiki Matsubara
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Hyogo, Japan
| | - Kento Kasahara
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Hyogo, Japan
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka 560-8531, Osaka, Japan
| | - Hisham M. Dokainish
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako 351-0198, Saitama, Japan
| | - Hiraku Oshima
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Hyogo, Japan
| | - Yuji Sugita
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Hyogo, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako 351-0198, Saitama, Japan
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe 650-0047, Hyogo, Japan
- Correspondence: ; Tel.: +81-48-462-1407
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33
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You X, Baiz CR. Importance of Hydrogen Bonding in Crowded Environments: A Physical Chemistry Perspective. J Phys Chem A 2022; 126:5881-5889. [PMID: 35968816 DOI: 10.1021/acs.jpca.2c03803] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cells are heterogeneous on every length and time scale; cytosol contains thousands of proteins, lipids, nucleic acids, and small molecules, and molecular interactions within this crowded environment determine the structure, dynamics, and stability of biomolecules. For decades, the effects of crowding at the atomistic scale have been overlooked in favor of more tractable models largely based on thermodynamics. Crowding can affect the conformations and stability of biomolecules by modulating water structure and dynamics within the cell, and these effects are nonlocal and environment dependent. Thus, characterizing water's hydrogen-bond (H-bond) networks is a critical step toward a complete microscopic crowding model. This perspective provides an overview of molecular crowding and describes recent time-resolved spectroscopy approaches investigating H-bond networks and dynamics in crowded or otherwise complex aqueous environments. Ultrafast spectroscopy combined with atomistic simulations has emerged as a powerful combination for studying H-bond structure and dynamics in heterogeneous multicomponent systems. We discuss the ongoing challenges toward developing a complete atomistic description of macromolecular crowding from an experimental as well as a theoretical perspective.
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Affiliation(s)
- Xiao You
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 19104, United States
| | - Carlos R Baiz
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 19104, United States
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34
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Ahmad F. Protein stability [determination] problems. Front Mol Biosci 2022; 9:880358. [PMID: 35992266 PMCID: PMC9388781 DOI: 10.3389/fmolb.2022.880358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Human health depends on the correct folding of proteins, for misfolding and aggregation lead to diseases. An unfolded (denatured) protein can refold to its original folded state. How does this occur is known as the protein folding problem. One of several related questions to this problem is that how much more stable is the folded state than the unfolded state. There are several measures of protein stability. In this article, protein stability is given a thermodynamic definition and is measured by Gibbs free energy change (ΔGD0) associated with the equilibrium, native (N) conformation ↔ denatured (D) conformation under the physiological condition usually taken as dilute buffer (or water) at 25 °C. We show that this thermodynamic quantity (ΔGD0), where subscript D represents transition between N and D states, and superscript 0 (zero) represents the fact that the transition occurs in the absence of denaturant, can be neither measured nor predicted under physiological conditions. However, ΔGD can be measured in the presence of strong chemical denaturants such as guanidinium chloride and urea which are shown to destroy all noncovalent interactions responsible for maintaining the folded structure. A problem with this measurement is that the estimate of ΔGD0 comes from the analysis of the plot of ΔGDversus denaturant concentration, which requires a long extrapolation of values of ΔGD, and all the three methods of extrapolation give three different values of ΔGD0 for a protein. Thus, our confidence in the authentic value of ΔGD0 is eroded. Another problem with this in vitro measurement of ΔGD0 is that it is done on the pure protein sample in dilute buffer which is a very large extrapolation of the in vivo conditions, for the crowding effect on protein stability is ignored.
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35
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Bae Y, Ha MY, Bang KT, Yang S, Kang SY, Kim J, Sung J, Kang S, Kang D, Lee WB, Choi TL, Park J. Conformation Dynamics of Single Polymer Strands in Solution. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2202353. [PMID: 35725274 DOI: 10.1002/adma.202202353] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/16/2022] [Indexed: 06/15/2023]
Abstract
Conformational changes in macromolecules significantly affect their functions and assembly into high-level structures. Despite advances in theoretical and experimental studies, investigations into the intrinsic conformational variations and dynamic motions of single macromolecules remain challenging. Here, liquid-phase transmission electron microscopy enables the real-time tracking of single-chain polymers. Imaging linear polymers, synthetically dendronized with conjugated aromatic groups, in organic solvent confined within graphene liquid cells, directly exhibits chain-resolved conformational dynamics of individual semiflexible polymers. These experimental and theoretical analyses reveal that the dynamic conformational transitions of the single-chain polymer originate from the degree of intrachain interactions. In situ observations also show that such dynamics of the single-chain polymer are significantly affected by environmental factors, including surfaces and interfaces.
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Affiliation(s)
- Yuna Bae
- School of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, Republic of Korea
- Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
| | - Min Young Ha
- School of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ki-Taek Bang
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sanghee Yang
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sung Yun Kang
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Joodeok Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, Republic of Korea
- Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
| | - Jongbaek Sung
- School of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, Republic of Korea
- Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
| | - Sungsu Kang
- School of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, Republic of Korea
- Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
| | - Dohun Kang
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Won Bo Lee
- School of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Tae-Lim Choi
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jungwon Park
- School of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, Republic of Korea
- Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- Institute of Engineering Research, Seoul National University, Seoul, 08826, Republic of Korea
- Advanced Institutes of Convergence Technology, Seoul National University, Suwon, Gyeonggi, 16229, Republic of Korea
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36
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Słyk E, Skóra T, Kondrat S. How macromolecules softness affects diffusion under crowding. SOFT MATTER 2022; 18:5366-5370. [PMID: 35833511 DOI: 10.1039/d2sm00357k] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Diffusion in a macromolecularly crowded environment is essential for many intracellular processes, from metabolism and catalysis to gene transcription and translation. So far, theoretical and experimental work has focused on anomalous subdiffusion, and the effects of interactions, shapes, and composition, while the compactness or softness of macromolecules has received less attention. Herein, we use Brownian dynamics simulations to study how the softness of crowders affects macromolecular diffusion. We find that in most cases, soft crowders slow down the diffusion less effectively than hard crowders like Ficoll. For instance, at a 30% occupied volume fraction, the diffusion in Ficoll70 is about 20% slower than in soft crowders of the same size. However, our simulations indicate that elongated macromolecules, such as double-stranded DNA pieces, can diffuse comparably or even faster in hard crowders. We relate these effects to the volume excluded by soft and hard crowders to different tracers. Our results show that the softness and shape of macromolecules are crucial factors determining diffusion under crowding, relevant to diverse intracellular environments.
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Affiliation(s)
- Edyta Słyk
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland.
- Department of Theoretical Chemistry, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Skłodowska University in Lublin, 20-031 Lublin, Poland
| | - Tomasz Skóra
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland.
| | - Svyatoslav Kondrat
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland.
- Max-Planck-Institut für Intelligente Systeme, Heisenbergstraße 3, 70569 Stuttgart, Germany
- IV. Institut für Theoretische Physik, Universität Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Institut für Computerphysik, Universität Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
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37
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Morimoto R, Horita M, Yamaguchi D, Nakai H, Nakano SI. Evaluation of Weak Interactions of Proteins and Organic Cations with DNA Duplex Structures. Biophys J 2022; 121:2873-2881. [PMID: 35791875 PMCID: PMC9388550 DOI: 10.1016/j.bpj.2022.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 11/02/2022] Open
Abstract
Molecular interactions and reactions in living cells occur with high background concentrations of organic compounds including proteins. Uncharged water-soluble polymers are commonly used cosolutes in studies on molecular crowding, and most studies argue about the effects of intracellular crowding based on results obtained using polymer cosolutes. Further investigations using protein crowders and organic cations are important in understanding the effects of cellular environments on nucleic acids with negatively charged surfaces. We assessed the effects of using model globular proteins, serum proteins, histone proteins, structurally flexible polypeptides, di- and polyamines, and uncharged polymers. Thermal stability analysis of DNA oligonucleotide structures revealed that unlike conventional polymer cosolutes, basic globular proteins (lysozyme and cytochrome c) at high concentrations stabilized long internal and bulge loop structures but not fully matched duplexes. The selective stabilization of long loop structures suggests preferential binding to unpaired nucleotides in loops through weak electrostatic interactions. Furthermore, the ability of the proteins to stabilize the loop structures was enhanced under macromolecular crowding conditions. Remarkably, the effects of basic proteins on the stability of fully matched duplexes were dissimilar to those of basic amino-acid-rich polypeptides and polyamines. This study provides new insights into the interaction of nucleic acid structures with organic cations.
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38
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Ahmed M, Ganesan A, Barakat K. Leveraging structural and 2D-QSAR to investigate the role of functional group substitutions, conserved surface residues and desolvation in triggering the small molecule-induced dimerization of hPD-L1. BMC Chem 2022; 16:49. [PMID: 35761353 PMCID: PMC9238240 DOI: 10.1186/s13065-022-00842-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 06/21/2022] [Indexed: 12/02/2022] Open
Abstract
Small molecules are rising as a new generation of immune checkpoints’ inhibitors, with compounds targeting the human Programmed death-ligand 1 (hPD-L1) protein are pioneering this area of research. Promising examples include the recently disclosed compounds from Bristol-Myers-Squibb (BMS). These molecules bind specifically to hPD-L1 through a unique mode of action. They induce dimerization between two hPD-L1 monomers through the hPD-1 binding interface in each monomer, thereby inhibiting the PD-1/PD-L1 axis. While the recently reported crystal structures of such small molecules bound to hPD-L1 reveal valuable insights regarding their molecular interactions, there is still limited information about the dynamics driving this unusual complex formation. The current study provides an in-depth computational structural analysis to study the interactions of five small molecule compounds in complex with hPD-L1. By employing a combination of molecular dynamic simulations, binding energy calculations and computational solvent mapping techniques, our analyses quantified the dynamic roles of different hydrophilic and lipophilic residues at the surface of hPD-L1 in mediating these interactions. Furthermore, ligand-based analyses, including Free-Wilson 2D-QSAR was conducted to quantify the impact of R-group substitutions at different sites of the phenoxy-methyl biphenyl core. Our results emphasize the importance of a terminal phenyl ring that must be present in any hPD-L1 small molecule inhibitor. This phenyl moiety overlaps with a very unfavorable hydration site, which can explain the ability of such small molecules to trigger hPD-L1 dimerization.
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Affiliation(s)
- Marawan Ahmed
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Aravindhan Ganesan
- ArGan's Lab, School of Pharmacy, University of Waterloo, Kitchener, ON, Canada
| | - Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada. .,Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada.
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Majumdar BB, Mondal J. Impact of Inert Crowders on Host-Guest Recognition Process. J Phys Chem B 2022; 126:4200-4215. [PMID: 35654414 DOI: 10.1021/acs.jpcb.2c01539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biological environments typically contain high concentrations (300-400 mg/mL) of different macromolecules at volume fractions as large as 30%-40%. Biomolecular recognition processes, a ubiquitous biological phenomena, occurring in such crowded heterogeneous media would differ significantly compared to the dilute buffer solutions. Here we quantify the potential impact of inert crowders on prototypical host-guest recognition process by explicit-solvent molecular dynamics (MD) simulations in atomic resolution. We demonstrate that the crowders, when smaller in size, would facilitate the binding process of the guest molecule by decreasing the free energy barrier for binding via excluded volume effect and desolvation of the host receptor. However, the extent of crowder-induced stabilization of a host-guest complex is found to be significantly higher when the guest molecule is sterically constricted to approach the host along a centrosymmetric direction, compared to its unrestricted, freely diffusive movement. A kinetic analysis of the recognition process reveals that the origin of a relatively stronger crowder impact during constricted movement of guest molecule lies in the relatively enhanced residence time of the guest inside the host by crowders. Together, our results suggest that the extent of impact of crowding on recognition processes would be contingent upon the presence or absence of constriction on ligand movement.
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Blackburn MR, Minkoff BB, Sussman MR. Mass spectrometry-based technologies for probing the 3D world of plant proteins. PLANT PHYSIOLOGY 2022; 189:12-22. [PMID: 35139210 PMCID: PMC9070838 DOI: 10.1093/plphys/kiac039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 12/30/2021] [Indexed: 05/03/2023]
Abstract
Over the past two decades, mass spectrometric (MS)-based proteomics technologies have facilitated the study of signaling pathways throughout biology. Nowhere is this needed more than in plants, where an evolutionary history of genome duplications has resulted in large gene families involved in posttranslational modifications and regulatory pathways. For example, at least 5% of the Arabidopsis thaliana genome (ca. 1,200 genes) encodes protein kinases and protein phosphatases that regulate nearly all aspects of plant growth and development. MS-based technologies that quantify covalent changes in the side-chain of amino acids are critically important, but they only address one piece of the puzzle. A more crucially important mechanistic question is how noncovalent interactions-which are more difficult to study-dynamically regulate the proteome's 3D structure. The advent of improvements in protein 3D technologies such as cryo-electron microscopy, nuclear magnetic resonance, and X-ray crystallography has allowed considerable progress to be made at this level, but these methods are typically limited to analyzing proteins, which can be expressed and purified in milligram quantities. Newly emerging MS-based technologies have recently been developed for studying the 3D structure of proteins. Importantly, these methods do not require protein samples to be purified and require smaller amounts of sample, opening the wider proteome for structural analysis in complex mixtures, crude lysates, and even in intact cells. These MS-based methods include covalent labeling, crosslinking, thermal proteome profiling, and limited proteolysis, all of which can be leveraged by established MS workflows, as well as newly emerging methods capable of analyzing intact macromolecules and the complexes they form. In this review, we discuss these recent innovations in MS-based "structural" proteomics to provide readers with an understanding of the opportunities they offer and the remaining challenges for understanding the molecular underpinnings of plant structure and function.
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Affiliation(s)
- Matthew R Blackburn
- Department of Biochemistry and Center for Genomic Science Innovation, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Benjamin B Minkoff
- Department of Biochemistry and Center for Genomic Science Innovation, University of Wisconsin, Madison, Wisconsin 53706, USA
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Liu D, Qiu Y, Li Q, Zhang H. Atomistic Simulation of Lysozyme in Solutions Crowded by Tetraethylene Glycol: Force Field Dependence. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27072110. [PMID: 35408509 PMCID: PMC9000840 DOI: 10.3390/molecules27072110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 11/16/2022]
Abstract
The behavior of biomolecules in crowded environments remains largely unknown due to the accuracy of simulation models and the limited experimental data for comparison. Here we chose a small crowder of tetraethylene glycol (PEG-4) to investigate the self-crowding of PEG-4 solutions and molecular crowding effects on the structure and diffusion of lysozyme at varied concentrations from dilute water to pure PEG-4 liquid. Two Amber-like force fields of Amber14SB and a99SB-disp were examined with TIP3P (fast diffusivity and low viscosity) and a99SB-disp (slow diffusivity and high viscosity) water models, respectively. Compared to the Amber14SB protein simulations, the a99SB-disp model yields more coordinated water and less PEG-4 molecules, less intramolecular hydrogen bonds (HBs), more protein-water HBs, and less protein-PEG HBs as well as stronger interactions and more hydrophilic and less hydrophobic contacts with solvent molecules. The a99SB-disp model offers comparable protein-solvent interactions in concentrated PEG-4 solutions to that in pure water. The PEG-4 crowding leads to a slow-down in the diffusivity of water, PEG-4, and protein, and the decline in the diffusion from atomistic simulations is close to or faster than the hard sphere model that neglects attractive interactions. Despite these differences, the overall structure of lysozyme appears to be maintained well at different PEG-4 concentrations for both force fields, except a slightly large deviation at 370 K at low concentrations with the a99SB-disp model. This is mainly attributed to the strong intramolecular interactions of the protein in the Amber14SB force field and to the large viscosity of the a99SB-disp water model. The results indicate that the protein force fields and the viscosity of crowder solutions affect the simulation of biomolecules under crowding conditions.
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Rivas G, Minton A. Influence of Nonspecific Interactions on Protein Associations: Implications for Biochemistry In Vivo. Annu Rev Biochem 2022; 91:321-351. [PMID: 35287477 DOI: 10.1146/annurev-biochem-040320-104151] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The cellular interior is composed of a variety of microenvironments defined by distinct local compositions and composition-dependent intermolecular interactions. We review the various types of nonspecific interactions between proteins and between proteins and other macromolecules and supramolecular structures that influence the state of association and functional properties of a given protein existing within a particular microenvironment at a particular point in time. The present state of knowledge is summarized, and suggestions for fruitful directions of research are offered. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Germán Rivas
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain;
| | - Allen Minton
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA;
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Kondrat S, von Lieres E. Mechanisms and Effects of Substrate Channelling in Enzymatic Cascades. Methods Mol Biol 2022; 2487:27-50. [PMID: 35687228 DOI: 10.1007/978-1-0716-2269-8_3] [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: 06/15/2023]
Abstract
Substrate or metabolite channelling is a transfer of intermediates produced by one enzyme to the sequential enzyme of a reaction cascade or metabolic pathway, without releasing them entirely into bulk. Despite an enormous effort and more than three decades of research, substrate channelling remains the subject of continuing debates and active investigation. Herein, we review the benefits and mechanisms of substrate channelling in vivo and in vitro. We discuss critically the effects that substrate channelling can have on enzymatic cascades, including speeding up or slowing down reaction cascades and protecting intermediates from sequestration and enzymes' surroundings from toxic or otherwise detrimental intermediates. We also discuss how macromolecular crowding affects substrate channelling and point out the galore of open questions.
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Affiliation(s)
- Svyatoslav Kondrat
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland.
- Max-Planck-Institut für Intelligente Systeme, Stuttgart, Germany.
- IV. Institut für Theoretische Physik, Universität Stuttgart, Stuttgart, Germany.
| | - Eric von Lieres
- Forschungszentrum Jülich, IBG-1: Biotechnology, Jülich, Germany
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44
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Shibata D, Kajimoto S, Nakabayashi T. Label-free tracking of intracellular molecular crowding with cell-cycle progression using Raman microscopy. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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45
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Skóra T, Popescu MN, Kondrat S. Conformation-changing enzymes and macromolecular crowding. Phys Chem Chem Phys 2021; 23:9065-9069. [PMID: 33885078 DOI: 10.1039/d0cp06631a] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We study how crowding affects the activity and catalysis-enhanced diffusion of enzymes and passive tracers by employing a fluctuating-dumbbell model of conformation-changing enzymes. Our Brownian dynamics simulations reveal that the diffusion of enzymes depends qualitatively on the type of crowding. If only enzymes are present in the system, the catalysis-induced enhancement of the enzyme diffusion - somewhat counter-intuitively - increases with crowding, while it decreases if crowding is due to inert particles. For the tracers, the diffusion enhancement increases with increasing the enzyme concentration. We also show how the enzyme activity is reduced by crowding and propose a simple expression to describe this reduction. Our results highlight subtle effects at play concerning enzymatic activity and macromolecular transport in crowded systems, such as, e.g., the interior of living cells.
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Affiliation(s)
- Tomasz Skóra
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland.
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46
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Modeling protein association from homogeneous to mixed environments: A reaction-diffusion dynamics approach. J Mol Graph Model 2021; 107:107936. [PMID: 34139641 DOI: 10.1016/j.jmgm.2021.107936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/30/2021] [Accepted: 04/26/2021] [Indexed: 11/21/2022]
Abstract
Protein-protein association in vivo occur in a crowded and complex environment. Theoretical models based on hard-core repulsion predict stabilization of the product under crowded conditions. Soft interactions, on the contrary, can either stabilize or destabilize the product formation. Here we modeled protein association in presence of crowders of varying size, shape, interaction potential and used different mixing parameters for constituent crowders to study the influence on the association reaction. It was found that size is a more dominant factor in crowder-induced stabilization than the shape. Furthermore, in a mixture of crowders having different sizes but identical interaction potential, the change of free energy is additive of the free energy changes produced by individual crowders. However, the free energy change is not additive if two crowders of same size interact via different interaction potentials. These findings provide a systematic understanding of crowding influences in heterogeneous medium.
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47
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Reinhardt M, Bruce NJ, Kokh DB, Wade RC. Brownian Dynamics Simulations of Proteins in the Presence of Surfaces: Long-Range Electrostatics and Mean-Field Hydrodynamics. J Chem Theory Comput 2021; 17:3510-3524. [PMID: 33784462 DOI: 10.1021/acs.jctc.0c01312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Simulations of macromolecular diffusion and adsorption in confined environments can offer valuable mechanistic insights into numerous biophysical processes. In order to model solutes at atomic detail on relevant time scales, Brownian dynamics simulations can be carried out with the approximation of rigid body solutes moving through a continuum solvent. This allows the precomputation of interaction potential grids for the solutes, thereby allowing the computationally efficient calculation of forces. However, hydrodynamic and long-range electrostatic interactions cannot be fully treated with grid-based approaches alone. Here, we develop a treatment of both hydrodynamic and electrostatic interactions to include the presence of surfaces by modeling grid-based and long-range interactions. We describe its application to simulate the self-association and many-molecule adsorption of the well-characterized protein hen egg-white lysozyme to mica-like and silica-like surfaces. We find that the computational model can recover a number of experimental observables of the adsorption process and provide insights into their determinants. The computational model is implemented in the Simulation of Diffusional Association (SDA) software package.
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Affiliation(s)
- Martin Reinhardt
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Neil J Bruce
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Daria B Kokh
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Center for Molecular Biology (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
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Feng C, Tan YL, Cheng YX, Shi YZ, Tan ZJ. Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement. Front Mol Biosci 2021; 8:666369. [PMID: 33928126 PMCID: PMC8078894 DOI: 10.3389/fmolb.2021.666369] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/17/2021] [Indexed: 12/27/2022] Open
Abstract
Macromolecules, such as RNAs, reside in crowded cell environments, which could strongly affect the folded structures and stability of RNAs. The emergence of RNA-driven phase separation in biology further stresses the potential functional roles of molecular crowding. In this work, we employed the coarse-grained model that was previously developed by us to predict 3D structures and stability of the mouse mammary tumor virus (MMTV) pseudoknot under different spatial confinements over a wide range of salt concentrations. The results show that spatial confinements can not only enhance the compactness and stability of MMTV pseudoknot structures but also weaken the dependence of the RNA structure compactness and stability on salt concentration. Based on our microscopic analyses, we found that the effect of spatial confinement on the salt-dependent RNA pseudoknot stability mainly comes through the spatial suppression of extended conformations, which are prevalent in the partially/fully unfolded states, especially at low ion concentrations. Furthermore, our comprehensive analyses revealed that the thermally unfolding pathway of the pseudoknot can be significantly modulated by spatial confinements, since the intermediate states with more extended conformations would loss favor when spatial confinements are introduced.
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Affiliation(s)
- Chenjie Feng
- Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, Center for Theoretical Physics, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Ya-Lan Tan
- Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, Center for Theoretical Physics, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Yu-Xuan Cheng
- Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, Center for Theoretical Physics, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Ya-Zhou Shi
- Research Center of Nonlinear Science, School of Mathematics and Computer Science, Wuhan Textile University, Wuhan, China
| | - Zhi-Jie Tan
- Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, Center for Theoretical Physics, School of Physics and Technology, Wuhan University, Wuhan, China
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49
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Su Z, Dhusia K, Wu Y. A multiscale study on the mechanisms of spatial organization in ligand-receptor interactions on cell surfaces. Comput Struct Biotechnol J 2021; 19:1620-1634. [PMID: 33868599 PMCID: PMC8026753 DOI: 10.1016/j.csbj.2021.03.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/21/2021] [Accepted: 03/21/2021] [Indexed: 01/11/2023] Open
Abstract
The binding of cell surface receptors with extracellular ligands triggers distinctive signaling pathways, leading into the corresponding phenotypic variation of cells. It has been found that in many systems, these ligand-receptor complexes can further oligomerize into higher-order structures. This ligand-induced oligomerization of receptors on cell surfaces plays an important role in regulating the functions of cell signaling. The underlying mechanism, however, is not well understood. One typical example is proteins that belong to the tumor necrosis factor receptor (TNFR) superfamily. Using a generic multiscale simulation platform that spans from atomic to subcellular levels, we compared the detailed physical process of ligand-receptor oligomerization for two specific members in the TNFR superfamily: the complex formed between ligand TNFα and receptor TNFR1 versus the complex formed between ligand TNFβ and receptor TNFR2. Interestingly, although these two systems share high similarity on the tertiary and quaternary structural levels, our results indicate that their oligomers are formed with very different dynamic properties and spatial patterns. We demonstrated that the changes of receptor’s conformational fluctuations due to the membrane confinements are closely related to such difference. Consistent to previous experiments, our simulations also showed that TNFR can preassemble into dimers prior to ligand binding, while the introduction of TNF ligands induced higher-order oligomerization due to a multivalent effect. This study, therefore, provides the molecular basis to TNFR oligomerization and reveals new insights to TNFR-mediated signal transduction. Moreover, our multiscale simulation framework serves as a prototype that paves the way to study higher-order assembly of cell surface receptors in many other bio-systems.
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Affiliation(s)
- Zhaoqian Su
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, United States
| | - Kalyani Dhusia
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, United States
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, United States
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50
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Iwakawa N, Morimoto D, Walinda E, Leeb S, Shirakawa M, Danielsson J, Sugase K. Transient Diffusive Interactions with a Protein Crowder Affect Aggregation Processes of Superoxide Dismutase 1 β-Barrel. J Phys Chem B 2021; 125:2521-2532. [PMID: 33657322 DOI: 10.1021/acs.jpcb.0c11162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Aggregate formation of superoxide dismutase 1 (SOD1) inside motor neurons is known as a major factor in onset of amyotrophic lateral sclerosis. The thermodynamic stability of the SOD1 β-barrel has been shown to decrease in crowded environments such as inside a cell, but it remains unclear how the thermodynamics of crowding-induced protein destabilization relate to SOD1 aggregation. Here we have examined the effects of a protein crowder, lysozyme, on fibril aggregate formation of the SOD1 β-barrel. We found that aggregate formation of SOD1 is decelerated even in mildly crowded solutions. Intriguingly, transient diffusive interactions with lysozyme do not significantly affect the static structure of the SOD1 β-barrel but stabilize an alternative excited "invisible" state. The net effect of crowding is to favor species off the aggregation pathway, thereby explaining the decelerated aggregation in the crowded environment. Our observations suggest that the intracellular environment may have a similar negative (inhibitory) effect on fibril formation of other amyloidogenic proteins in living cells. Deciphering how crowded intracellular environments affect aggregation and fibril formation of such disease-associated proteins will probably become central in understanding the exact role of aggregation in the etiology of these enigmatic diseases.
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Affiliation(s)
- Naoto Iwakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Daichi Morimoto
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Sarah Leeb
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Masahiro Shirakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Jens Danielsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Kenji Sugase
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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