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Moldovean-Cioroianu NS. Reviewing the Structure-Function Paradigm in Polyglutamine Disorders: A Synergistic Perspective on Theoretical and Experimental Approaches. Int J Mol Sci 2024; 25:6789. [PMID: 38928495 PMCID: PMC11204371 DOI: 10.3390/ijms25126789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Polyglutamine (polyQ) disorders are a group of neurodegenerative diseases characterized by the excessive expansion of CAG (cytosine, adenine, guanine) repeats within host proteins. The quest to unravel the complex diseases mechanism has led researchers to adopt both theoretical and experimental methods, each offering unique insights into the underlying pathogenesis. This review emphasizes the significance of combining multiple approaches in the study of polyQ disorders, focusing on the structure-function correlations and the relevance of polyQ-related protein dynamics in neurodegeneration. By integrating computational/theoretical predictions with experimental observations, one can establish robust structure-function correlations, aiding in the identification of key molecular targets for therapeutic interventions. PolyQ proteins' dynamics, influenced by their length and interactions with other molecular partners, play a pivotal role in the polyQ-related pathogenic cascade. Moreover, conformational dynamics of polyQ proteins can trigger aggregation, leading to toxic assembles that hinder proper cellular homeostasis. Understanding these intricacies offers new avenues for therapeutic strategies by fine-tuning polyQ kinetics, in order to prevent and control disease progression. Last but not least, this review highlights the importance of integrating multidisciplinary efforts to advancing research in this field, bringing us closer to the ultimate goal of finding effective treatments against polyQ disorders.
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Affiliation(s)
- Nastasia Sanda Moldovean-Cioroianu
- Institute of Materials Science, Bioinspired Materials and Biosensor Technologies, Kiel University, Kaiserstraße 2, 24143 Kiel, Germany;
- Faculty of Physics, Babeș-Bolyai University, Kogălniceanu 1, RO-400084 Cluj-Napoca, Romania
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2
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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: 15] [Impact Index Per Article: 15.0] [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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3
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Phan TM, Schmit JD. Conformational entropy limits the transition from nucleation to elongation in amyloid aggregation. Biophys J 2022; 121:2931-2939. [PMID: 35778843 PMCID: PMC9388551 DOI: 10.1016/j.bpj.2022.06.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/11/2022] [Accepted: 06/17/2022] [Indexed: 11/30/2022] Open
Abstract
The formation of β-sheet rich amyloid fibrils in Alzheimer's disease and other neurodegenerative disorders is limited by a slow nucleation event. To understand the initial formation of β-sheets from disordered peptides, we used all-atom simulations to parameterize a lattice model that treats each amino acid as a binary variable with β and non-β states. We show that translational and conformational entropy give the nascent β-sheet an anisotropic surface tension which can be used to describe the nucleus with two-dimensional Classical Nucleation Theory. Since translational entropy depends on concentration, the aspect ratio of the critical β-sheet changes with protein concentration. Our model explains the transition from the nucleation phase to elongation as the point where the β-sheet core becomes large enough to overcome the conformational entropy cost to straighten the terminal molecule. At this point the β-strands in the nucleus spontaneously elongate, which results in a larger binding surface to capture new molecules. These results suggest that nucleation is relatively insensitive to sequence differences in co-aggregation experiments because the nucleus only involves a small portion of the peptide.
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Affiliation(s)
- Tien M Phan
- Department of Physics, Kansas State University, Manhattan, KS 66506, USA
| | - Jeremy D Schmit
- Department of Physics, Kansas State University, Manhattan, KS 66506, USA.
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4
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Chávez-García C, Hénin J, Karttunen M. Multiscale Computational Study of the Conformation of the Full-Length Intrinsically Disordered Protein MeCP2. J Chem Inf Model 2022; 62:958-970. [PMID: 35130441 DOI: 10.1021/acs.jcim.1c01354] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The malfunction of the methyl-CpG binding protein 2 (MeCP2) is associated with the Rett syndrome, one of the most common causes of cognitive impairment in females. MeCP2 is an intrinsically disordered protein (IDP), making its experimental characterization a challenge. There is currently no structure available for the full-length MeCP2 in any of the databases, and only the structure of its MBD domain has been solved. We used this structure to build a full-length model of MeCP2 by completing the rest of the protein via ab initio modeling. Using a combination of all-atom and coarse-grained simulations, we characterized its structure and dynamics as well as the conformational space sampled by the ID and transcriptional repression domain (TRD) domains in the absence of the rest of the protein. The present work is the first computational study of the full-length protein. Two main conformations were sampled in the coarse-grained simulations: a globular structure similar to the one observed in the all-atom force field and a two-globule conformation. Our all-atom model is in good agreement with the available experimental data, predicting amino acid W104 to be buried, amino acids R111 and R133 to be solvent-accessible, and having a 4.1% α-helix content, compared to the 4% found experimentally. Finally, we compared the model predicted by AlphaFold to our Modeller model. The model was not stable in water and underwent further folding. Together, these simulations provide a detailed (if perhaps incomplete) conformational ensemble of the full-length MeCP2, which is compatible with experimental data and can be the basis of further studies, e.g., on mutants of the protein or its interactions with its biological partners.
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Affiliation(s)
- Cecilia Chávez-García
- Department of Chemistry, the University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,The Centre of Advanced Materials and Biomaterials Research, the University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Jérôme Hénin
- Laboratoire de Biochimie Théorique UPR 9080, CNRS and Université de Paris, Paris 75005, France
| | - Mikko Karttunen
- Department of Chemistry, the University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,The Centre of Advanced Materials and Biomaterials Research, the University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,Department of Physics and Astronomy, the University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7, Canada
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5
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Szała-Mendyk B, Molski A. Diverse Aggregation Kinetics Predicted by a Coarse-Grained Peptide Model. J Phys Chem B 2021; 125:7587-7597. [PMID: 34251838 PMCID: PMC8389928 DOI: 10.1021/acs.jpcb.1c00290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
![]()
Protein and peptide
aggregation is a ubiquitous phenomenon with
implications in medicine, pharmaceutical industry, and materials science.
An important issue in peptide aggregation is the molecular mechanism
of aggregate nucleation and growth. In many experimental studies,
sigmoidal kinetics curves show a clear lag phase ascribed to nucleation;
however, experimental studies also show downhill kinetics curves,
where the monomers decay continuously and no lag phase can be seen.
In this work, we study peptide aggregation kinetics using a coarse-grained
implicit solvent model introduced in our previous work. Our simulations
explore the hypothesis that the interplay between interchain attraction
and intrachain bending stiffness controls the aggregation kinetics
and transient aggregate morphologies. Indeed, our model reproduces
the aggregation modes seen in experiment: no observed aggregation,
nucleated aggregation, and rapid downhill aggregation. We find that
the interaction strength is the primary parameter determining the
aggregation mode, whereas the stiffness is a secondary parameter modulating
the transient morphologies and aggregation rates: more attractive
and stiff chains aggregate more rapidly and the transient morphologies
are more ordered. We also explore the effects of the initial monomer
concentration and the chain length. As the concentration decreases,
the aggregation mode shifts from downhill to nucleated and no-aggregation.
This concentration effect is in line with an experimental observation
that the transition between downhill and nucleated kinetics is concentration-dependent.
We find that longer peptides can aggregate at conditions where short
peptides do not aggregate at all. It supports an experimental observation
that the elongation of a homopeptide, e.g., polyglutamine, can increase
the aggregation propensity.
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Affiliation(s)
- Beata Szała-Mendyk
- Faculty of Chemistry, Adam Mickiewicz University in Poznań, Umultowska 89b, 61-614 Poznań, Poland
| | - Andrzej Molski
- Faculty of Chemistry, Adam Mickiewicz University in Poznań, Umultowska 89b, 61-614 Poznań, Poland
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6
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Barrera EE, Zonta F, Pantano S. Dissecting the role of glutamine in seeding peptide aggregation. Comput Struct Biotechnol J 2021; 19:1595-1602. [PMID: 33868596 PMCID: PMC8039506 DOI: 10.1016/j.csbj.2021.02.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/18/2021] [Accepted: 02/20/2021] [Indexed: 12/02/2022] Open
Abstract
Poly glutamine and glutamine-rich peptides play a central role in a plethora of pathological aggregation events. However, biophysical characterization of soluble oligomers -the most toxic species involved in these processes- remains elusive due to their structural heterogeneity and dynamical nature. Here, we exploit the high spatio-temporal resolution of coarse-grained simulations as a computational microscope to characterize the aggregation propensity and morphology of a series of polyglutamine and glutamine-rich peptides. Comparative analysis of ab-initio aggregation pinpointed a double role for glutamines. In the first phase, glutamines mediate seeding by pairing monomeric peptides, which serve as primers for higher-order nucleation. According to the glutamine content, these low molecular-weight oligomers may then proceed to create larger aggregates. Once within the aggregates, buried glutamines continue to play a role in their maturation by optimizing solvent-protected hydrogen bonds networks.
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Affiliation(s)
- Exequiel E. Barrera
- Instituto de Histología y Embriología (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CC56, Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina
| | - Francesco Zonta
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Sergio Pantano
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, CP 11400 Montevideo, Uruguay
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7
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Gaughran SK, Rickman JM, Haaga J, Gunton JD. Monte Carlo simulations of patch models with applications to soft matter. SOFT MATTER 2020; 16:8628-8638. [PMID: 32844865 DOI: 10.1039/d0sm01110j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Patch models have been employed to describe anisotropic interactions in disparate soft matter systems. In this work, we present a unified study of a patch model to explore particle self-assembly in both monodisperse and polydisperse systems, with applications to both proteins and colloids. In the first case, we obtained a temperature-density phase diagram for a model of the protein polyglutamine from Monte Carlo simulations. These simulations evinced clusters in the gas phase and, via a comparison with the corresponding coarse-grained PLUM model for this system, we verified that dense clustering in the gas phase falls into the supersaturation region of the saturation curve. In the second case, we have investigated the effect of size polydispersity on the phase behavior of binary colloidal mixtures. It was found that the width of gas-liquid phase coexistence increases with increasing polydispersity and that, in addition to the aforementioned particle clustering, small particles decorate patches on large particles, thereby creating large-particle bridges. Our aim is to compare and contrast self-assembly in these two prototypical systems.
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Affiliation(s)
- S K Gaughran
- Department of Physics, Lehigh University, Bethlehem, PA 18015, USA.
| | - J M Rickman
- Department of Physics, Lehigh University, Bethlehem, PA 18015, USA. and Department of Materials Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - J Haaga
- Department of Physics, Lehigh University, Bethlehem, PA 18015, USA.
| | - J D Gunton
- Department of Physics, Lehigh University, Bethlehem, PA 18015, USA.
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8
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Szała-Mendyk B, Molski A. Clustering and Fibril Formation during GNNQQNY Aggregation: A Molecular Dynamics Study. Biomolecules 2020; 10:biom10101362. [PMID: 32987720 PMCID: PMC7598727 DOI: 10.3390/biom10101362] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 12/02/2022] Open
Abstract
The precise kinetic pathways of peptide clustering and fibril formation are not fully understood. Here we study the initial clustering kinetics and transient cluster morphologies during aggregation of the heptapeptide fragment GNNQQNY from the yeast prion protein Sup35. We use a mid-resolution coarse-grained molecular dynamics model of Bereau and Deserno to explore the aggregation pathways from the initial random distribution of free monomers to the formation of large clusters. By increasing the system size to 72 peptides we could follow directly the molecular events leading to the formation of stable fibril-like structures. To quantify those structures we developed a new cluster helicity parameter. We found that the formation of fibril-like structures is a cooperative processes that requires a critical number of monomers, M⋆≈25, in a cluster. The terminal tyrosine residue is the structural determinant in the formation of helical fibril-like structures. This work supports and quantifies the two-step aggregation model where the initially formed amorphous clusters grow and, when they are large enough, rearrange into mature twisted structures. However, in addition to the nucleated fibrillation, growing aggregates undergo further internal reorganization, which leads to more compact structures of large aggregates.
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Kashchiev D. Growth probability and formation time of the individual Oosawa-Kasai protein fibril. Phys Rev E 2018; 98:012412. [PMID: 30110800 DOI: 10.1103/physreve.98.012412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Indexed: 12/23/2022]
Abstract
Protein fibrils are currently of great academic and practical interest because of their involvement in scores of severe human diseases and their promising use in various high-technology devices. The Oosawa-Kasai (OK) model of protein self-assembly into fibrils has been widely used to gain mechanistic insight into the process of fibril formation and growth. Here this model is employed to obtain exact and mathematically simple expressions for the probability P_{n} of an individual fibril of n protein monomers to grow to a macroscopically large size and for the mean time τ_{n} that such a fibril needs for its formation. These expressions quantify the increase of P_{n} and the decrease of τ_{n} with increasing the concentration of monomeric protein in the solution. When used for analysis of experimental P_{n} and τ_{n} data, they make it possible to determine the parameters characterizing fibril nucleation and growth in the framework of the OK model. Finally, an expression is found for the mean time of the first appearance of an n-sized fibril in the protein solution. The results obtained are applicable to the formation of other aggregates corresponding to the OK fibrils, such as the one-dimensional Kossel-Stranski crystals and Ising ferromagnets.
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Affiliation(s)
- Dimo Kashchiev
- Institute of Physical Chemistry, Bulgarian Academy of Sciences, ul. Acad. G. Bonchev 11, Sofia 1113, Bulgaria
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