1
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Mioduszewski Ł. Choosing the right density for a concentrated protein system like gluten in a coarse-grained model. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:583-591. [PMID: 37378869 PMCID: PMC10618313 DOI: 10.1007/s00249-023-01667-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 05/05/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023]
Abstract
Large coarse-grained simulations are often conducted with an implicit solvent, which makes it hard to assess the water content of the sample and the effective concentration of the system. Here the number and the size of cavities and entanglements in the system, together with density profiles, are used to asses the homogeneity and interconnectedness of gluten. This is a continuation of an earlier article, "Viscoelastic properties of wheat gluten in a molecular dynamics study" (Mioduszewski and Cieplak 2021b). It turns out there is a wide range of densities (between 1 residue per cubic nanometer and 3 residues/nm[Formula: see text]) where the system is interconnected, but not homogeneous: there are still large empty spaces, surrounded by an entangled protein network. Those findings should be of importance to any coarse-grained simulation of large protein systems.
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Affiliation(s)
- Łukasz Mioduszewski
- Faculty of Mathematics and Natural Sciences, Cardinal Stefan Wyszyński University, Wóycickiego 1/3, 01-938, Warsaw, Poland.
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2
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Szała-Mendyk B, Phan TM, Mohanty P, Mittal J. Challenges in studying the liquid-to-solid phase transitions of proteins using computer simulations. Curr Opin Chem Biol 2023; 75:102333. [PMID: 37267850 PMCID: PMC10527940 DOI: 10.1016/j.cbpa.2023.102333] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/24/2023] [Accepted: 04/30/2023] [Indexed: 06/04/2023]
Abstract
"Membraneless organelles," also referred to as biomolecular condensates, perform a variety of cellular functions and their dysregulation is implicated in cancer and neurodegeneration. In the last two decades, liquid-liquid phase separation (LLPS) of intrinsically disordered and multidomain proteins has emerged as a plausible mechanism underlying the formation of various biomolecular condensates. Further, the occurrence of liquid-to-solid transitions within liquid-like condensates may give rise to amyloid structures, implying a biophysical link between phase separation and protein aggregation. Despite significant advances, uncovering the microscopic details of liquid-to-solid phase transitions using experiments remains a considerable challenge and presents an exciting opportunity for the development of computational models which provide valuable, complementary insights into the underlying phenomenon. In this review, we first highlight recent biophysical studies which provide new insights into the molecular mechanisms underlying liquid-to-solid (fibril) phase transitions of folded, disordered and multi-domain proteins. Next, we summarize the range of computational models used to study protein aggregation and phase separation. Finally, we discuss recent computational approaches which attempt to capture the underlying physics of liquid-to-solid transitions along with their merits and shortcomings.
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Affiliation(s)
- Beata Szała-Mendyk
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, TAMU 3127, College Station, 77843, Texas, United States.
| | - Tien Minh Phan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, TAMU 3127, College Station, 77843, Texas, United States.
| | - Priyesh Mohanty
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, TAMU 3127, College Station, 77843, Texas, United States.
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, TAMU 3127, College Station, 77843, Texas, United States; Department of Chemistry, Texas A&M University, TAMU 3255, College Station, 77843, Texas, United States; Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, TAMU 3255, College Station, 77843, Texas, United States.
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3
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Pham DQH, Chwastyk M, Cieplak M. The coexistence region in the Van der Waals fluid and the liquid-liquid phase transitions. Front Chem 2023; 10:1106599. [PMID: 36760519 PMCID: PMC9905123 DOI: 10.3389/fchem.2022.1106599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/29/2022] [Indexed: 01/26/2023] Open
Abstract
Cellular membraneless organelles are thought to be droplets formed within the two-phase region corresponding to proteinaceous systems endowed with the liquid-liquid transition. However, their metastability requires an additional constraint-they arise in a certain region of density and temperature between the spinodal and binodal lines. Here, we consider the well-studied van der Waals fluid as a test model to work out criteria to determine the location of the spinodal line for situations in which the equation of state is not known. Our molecular dynamics studies indicate that this task can be accomplished by considering the specific heat, the surface tension and characteristics of the molecular clusters, such as the number of component chains and radius of gyration.
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Affiliation(s)
| | - Mateusz Chwastyk
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
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4
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Szała-Mendyk B, Molski A. Side Chain Geometry Determines the Fibrillation Propensity of a Minimal Two-Beads-per-Residue Peptide Model. J Phys Chem B 2022; 126:5772-5780. [PMID: 35917439 PMCID: PMC9376954 DOI: 10.1021/acs.jpcb.2c03502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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The molecular mechanism of fibrillation is an important
issue for
understanding peptide aggregation. In our previous work, we demonstrated
that the interchain attraction and intrachain bending stiffness control
the aggregation kinetics and transient aggregate morphologies of a
one-bead-per-residue implicit solvent peptide model. However, that
model did not lead to fibrillation. In this work, we study the molecular
origin of fibril formation using a two-beads-per-residue model, where
one bead represents the backbone residue atoms and the other the side
chain atoms. We show that the side chain geometry determines the fibrillation
propensity that is further modulated by the modified terminal beads.
This allows us to bring out the effects of side chain geometry and
terminal capping on the fibrillation propensity. Our model does not
assume a secondary structure and is, perhaps, the simplest bead-based
chain model leading to fibrillation.
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Affiliation(s)
- Beata Szała-Mendyk
- Faculty of Chemistry, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland
| | - Andrzej Molski
- Faculty of Chemistry, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland
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5
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Cieplak M, Mioduszewski Ł, Chwastyk M. Contact-Based Analysis of Aggregation of Intrinsically Disordered Proteins. Methods Mol Biol 2022; 2340:105-120. [PMID: 35167072 DOI: 10.1007/978-1-0716-1546-1_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We review the contact-based description of aggregation of intrinsically disordered proteins in coarse-grained and all-atom models. We consider polyglutamines and polyalanines at various concentrations of the peptides. We also study associations of two chains of α-synuclein and up to 20 chains of a 12-residue-long segment of protein tau. We demonstrate that the total number of two-chain association events (in an aggregate that comprises at least two chains) provides a useful measure of the propensity to aggregate. This measure is consistent, for instance, with the previously reported mass spectroscopy data. The distribution of the number of association events is given essentially by a power law as a function of the duration of these events. The corresponding exponent depends on the protein and the temperature but not on the concentration of the proteins.
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Affiliation(s)
- Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
| | | | - Mateusz Chwastyk
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
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6
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Co NT, Li MS, Krupa P. Computational Models for the Study of Protein Aggregation. Methods Mol Biol 2022; 2340:51-78. [PMID: 35167070 DOI: 10.1007/978-1-0716-1546-1_4] [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: 06/14/2023]
Abstract
Protein aggregation has been studied by many groups around the world for many years because it can be the cause of a number of neurodegenerative diseases that have no effective treatment. Obtaining the structure of related fibrils and toxic oligomers, as well as describing the pathways and main factors that govern the self-organization process, is of paramount importance, but it is also very difficult. To solve this problem, experimental and computational methods are often combined to get the most out of each method. The effectiveness of the computational approach largely depends on the construction of a reasonable molecular model. Here we discussed different versions of the four most popular all-atom force fields AMBER, CHARMM, GROMOS, and OPLS, which have been developed for folded and intrinsically disordered proteins, or both. Continuous and discrete coarse-grained models, which were mainly used to study the kinetics of aggregation, are also summarized.
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Affiliation(s)
- Nguyen Truong Co
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
- Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam
| | - Pawel Krupa
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
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7
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Nguyen PH, Derreumaux P. Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation. Methods Mol Biol 2022; 2340:175-196. [PMID: 35167075 DOI: 10.1007/978-1-0716-1546-1_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein aggregation can lead to well-defined structures that are functional, but is also the cause of the death of neuron cells in many neurodegenerative diseases. The complexity of the molecular events involved in the aggregation kinetics of amyloid proteins and the transient and heterogeneous characters of all oligomers prevent high-resolution structural experiments. As a result, computer simulations have been used to determine the atomic structures of amyloid proteins at different association stages as well as to understand fibril dissociation. In this chapter, we first review the current computer simulation methods used for aggregation with some atomistic and coarse-grained results aimed at better characterizing the early formed oligomers and amyloid fibril formation. Then we present the applications of non-equilibrium molecular dynamics simulations to comprehend the dissociation of protein assemblies.
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Affiliation(s)
- Phuong H Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université de Paris, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université de Paris, Paris, France.
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France.
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8
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Mioduszewski Ł, Cieplak M. Viscoelastic properties of wheat gluten in a molecular dynamics study. PLoS Comput Biol 2021; 17:e1008840. [PMID: 33760823 PMCID: PMC8021197 DOI: 10.1371/journal.pcbi.1008840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 04/05/2021] [Accepted: 02/28/2021] [Indexed: 11/19/2022] Open
Abstract
Wheat (Triticum spp.) gluten consists mainly of intrinsincally disordered storage proteins (glutenins and gliadins) that can form megadalton-sized networks. These networks are responsible for the unique viscoelastic properties of wheat dough and affect the quality of bread. These properties have not yet been studied by molecular level simulations. Here, we use a newly developed α-C-based coarse-grained model to study ∼ 4000-residue systems. The corresponding time-dependent properties are studied through shear and axial deformations. We measure the response force to the deformation, the number of entanglements and cavities, the mobility of residues, the number of the inter-chain bonds, etc. Glutenins are shown to influence the mechanics of gluten much more than gliadins. Our simulations are consistent with the existing ideas about gluten elasticity and emphasize the role of entanglements and hydrogen bonding. We also demonstrate that the storage proteins in maize and rice lead to weaker elasticity which points to the unique properties of wheat gluten. During the breadmaking process, expanding gas bubbles cause the dough to increase volume. Gluten proteins act as an elastic scaffold in that process, allowing the wheat dough to grow more than other kinds of dough. Thus, explaining the unique viscoelastic properties of gluten at the molecular level may be of great interest to the baking industry. Assessing the structural properties of gluten is difficult because its proteins are disordered. We provide the first molecular dynamics model of gluten elasticity, that is able to distinguish gluten and proteins from different plants, like maize and rice. Our model shows the structural changes the gluten proteins undergo during their deformation, which mimics the mixing of dough during kneading. It also allows for a determination of the force required to extend gluten proteins, as during baking. The data confirms existing theories about gluten, but it also provides molecular-level information about the extraordinary elasticity of gluten.
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Affiliation(s)
| | - Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
- * E-mail:
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9
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Ivanova MI, Lin Y, Lee YH, Zheng J, Ramamoorthy A. Biophysical processes underlying cross-seeding in amyloid aggregation and implications in amyloid pathology. Biophys Chem 2021; 269:106507. [PMID: 33254009 PMCID: PMC10317075 DOI: 10.1016/j.bpc.2020.106507] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/13/2020] [Accepted: 11/13/2020] [Indexed: 12/18/2022]
Abstract
Abnormal aggregation of proteins into filamentous aggregates commonly associates with many diseases, such as Alzheimer's disease, Parkinson's disease and type-2 diabetes. These filamentous aggregates, also known as amyloids, can propagate their abnormal structures to either the same precursor molecules (seeding) or other protein monomers (cross-seeding). Cross-seeding has been implicated in the abnormal protein aggregation and has been found to facilitate the formation of physiological amyloids. It has risen to be an exciting area of research with a high volume of published reports. In this review article, we focus on the biophysical processes underlying the cross-seeding for some of the most commonly studied amyloid proteins. Here we will discuss the relevant literature related to cross-seeded polymerization of amyloid-beta, human islet amyloid polypeptide (hIAPP, or also known as amylin) and alpha-synuclein. SEVI (semen-derived enhancer of viral infection) amyloid formation by the cross-seeding between the bacterial curli protein and PAP248-286 is also briefly discussed.
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Affiliation(s)
- Magdalena I Ivanova
- Neurology, University of Michigan, Ann Arbor, MI 48109, USA; Biophysics, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Yuxi Lin
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, Chungbuk 28119, South Korea
| | - Young-Ho Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, Chungbuk 28119, South Korea; Bio-Analytical Science, University of Science and Technology, Daejeon 34113, South Korea; Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, South Korea; Research headquarters, Korea Brain Research Institute, Daegu 41068, South Korea
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Ohio, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
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10
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Plant isoquinoline alkaloids as potential neurodrugs: A comparative study of the effects of benzo[c]phenanthridine and berberine-based compounds on β-amyloid aggregation. Chem Biol Interact 2020; 334:109300. [PMID: 33098838 PMCID: PMC7577920 DOI: 10.1016/j.cbi.2020.109300] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/17/2020] [Accepted: 10/21/2020] [Indexed: 12/15/2022]
Abstract
Herein we present a comparative study of the effects of isoquinoline alkaloids belonging to benzo[c]phenanthridine and berberine families on β-amyloid aggregation. Results obtained using a Thioflavine T (ThT) fluorescence assay and circular dichroism (CD) spectroscopy suggested that the benzo[c]phenanthridine nucleus, present in both sanguinarine and chelerythrine molecules, was directly involved in an inhibitory effect of Aβ1-42 aggregation. Conversely, coralyne, that contains the isomeric berberine nucleus, significantly increased propensity for Aβ1-42 to aggregate. Surface Plasmon Resonance (SPR) experiments provided quantitative estimation of these interactions: coralyne bound to Aβ1-42 with an affinity (KD = 11.6 μM) higher than benzo[c]phenanthridines. Molecular docking studies confirmed that all three compounds are able to recognize Aβ1-42 in different aggregation forms suggesting their effective capacity to modulate the Aβ1-42 self-recognition mechanism. Molecular dynamics simulations indicated that coralyne increased the β-content of Aβ1-42, in early stages of aggregation, consistent with fluorescence-based promotion of the Aβ1-42 self-recognition mechanism by this alkaloid. At the same time, sanguinarine induced Aβ1-42 helical conformation corroborating its ability to delay aggregation as experimentally proved in vitro. The investigated compounds were shown to interfere with aggregation of Aβ1-42 demonstrating their potential as starting leads for the development of therapeutic strategies in neurodegenerative diseases.
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Mioduszewski Ł, Różycki B, Cieplak M. Pseudo-Improper-Dihedral Model for Intrinsically Disordered Proteins. J Chem Theory Comput 2020; 16:4726-4733. [PMID: 32436706 PMCID: PMC7588027 DOI: 10.1021/acs.jctc.0c00338] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We present a new coarse-grained Cα-based protein model with a nonradial multibody pseudo-improper-dihedral potential that is transferable, time-independent, and suitable for molecular dynamics. It captures the nature of backbone and side-chain interactions between amino acid residues by adapting a simple improper dihedral term for a one-bead-per-residue model. It is parameterized for intrinsically disordered proteins and applicable to simulations of such proteins and their assemblies on millisecond time scales.
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Affiliation(s)
- Łukasz Mioduszewski
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
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