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Kamagata K, Ariefai M, Takahashi H, Hando A, Subekti DRG, Ikeda K, Hirano A, Kameda T. Rational peptide design for regulating liquid-liquid phase separation on the basis of residue-residue contact energy. Sci Rep 2022; 12:13718. [PMID: 35962177 PMCID: PMC9374670 DOI: 10.1038/s41598-022-17829-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/01/2022] [Indexed: 12/13/2022] Open
Abstract
Since liquid-liquid phase separation (LLPS) of proteins is governed by their intrinsically disordered regions (IDRs), it can be controlled by LLPS-regulators that bind to the IDRs. The artificial design of LLPS-regulators based on this mechanism can be leveraged in biological and therapeutic applications. However, the fabrication of artificial LLPS-regulators remains challenging. Peptides are promising candidates for artificial LLPS-regulators because of their ability to potentially bind to IDRs complementarily. In this study, we provide a rational peptide design methodology for targeting IDRs based on residue-residue contact energy obtained using molecular dynamics (MD) simulations. This methodology provides rational peptide sequences that function as LLPS regulators. The peptides designed with the MD-based contact energy showed dissociation constants of 35-280 nM for the N-terminal IDR of the tumor suppressor p53, which are significantly lower than the dissociation constants of peptides designed with the conventional 3D structure-based energy, demonstrating the validity of the present peptide design methodology. Importantly, all of the designed peptides enhanced p53 droplet formation. The droplet-forming peptides were converted to droplet-deforming peptides by fusing maltose-binding protein (a soluble tag) to the designed peptides. Thus, the present peptide design methodology for targeting IDRs is useful for regulating droplet formation.
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Affiliation(s)
- Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan. .,Department of Chemistry, Faculty of Science, Tohoku University, Sendai, 980-8578, Japan. .,Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan.
| | - Maulana Ariefai
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.,Department of Chemistry, Faculty of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Hiroto Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Atsumi Hando
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.,Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Dwiky Rendra Graha Subekti
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Keisuke Ikeda
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan
| | - Atsushi Hirano
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8565, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Koto, Tokyo, 135-0064, Japan.
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Bianco V, Franzese G, Coluzza I. In Silico Evidence That Protein Unfolding is a Precursor of Protein Aggregation. Chemphyschem 2020; 21:377-384. [DOI: 10.1002/cphc.201900904] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/01/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Valentino Bianco
- Faculty of Chemistry, Chemical Physics Department, Universidad Complutense de Madrid, Plaza de las Ciencias Ciudad Universitaria Madrid 28040 Spain
| | - Giancarlo Franzese
- Secció de Física Estadística i Interdisciplinària-Departament de Física de la Matèria Condensada, Facultat de Física & Institute of Nanoscience and Nanotechnology (IN2UB) Universitat de Barcelona Martí i Franquès 1 08028 Barcelona Spain
| | - Ivan Coluzza
- CIC biomaGUNE Paseo Miramon 182 20014 San Sebastian Spain
- IKERBASQUE, Basque Foundation for Science 48013 Bilbao Spain
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Pandey RB, Farmer BL. Aggregation and network formation in self-assembly of protein (H3.1) by a coarse-grained Monte Carlo simulation. J Chem Phys 2014; 141:175103. [PMID: 25381549 DOI: 10.1063/1.4901129] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Multi-scale aggregation to network formation of interacting proteins (H3.1) are examined by a knowledge-based coarse-grained Monte Carlo simulation as a function of temperature and the number of protein chains, i.e., the concentration of the protein. Self-assembly of corresponding homo-polymers of constitutive residues (Cys, Thr, and Glu) with extreme residue-residue interactions, i.e., attractive (Cys-Cys), neutral (Thr-Thr), and repulsive (Glu-Glu), are also studied for comparison with the native protein. Visual inspections show contrast and similarity in morphological evolutions of protein assembly, aggregation of small aggregates to a ramified network from low to high temperature with the aggregation of a Cys-polymer, and an entangled network of Glu and Thr polymers. Variations in mobility profiles of residues with the concentration of the protein suggest that the segmental characteristic of proteins is altered considerably by the self-assembly from that in its isolated state. The global motion of proteins and Cys polymer chains is enhanced by their interacting network at the low temperature where isolated chains remain quasi-static. Transition from globular to random coil transition, evidenced by the sharp variation in the radius of gyration, of an isolated protein is smeared due to self-assembly of interacting networks of many proteins. Scaling of the structure factor S(q) with the wave vector q provides estimates of effective dimension D of the mass distribution at multiple length scales in self-assembly. Crossover from solid aggregates (D ∼ 3) at low temperature to a ramified fibrous network (D ∼ 2) at high temperature is observed for the protein H3.1 and Cys polymers in contrast to little changes in mass distribution (D ∼ 1.6) of fibrous Glu- and Thr-chain configurations.
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Affiliation(s)
- R B Pandey
- Department of Physics and Astronomy, University of Southern Mississippi, Hattiesburg, Mississippi 39406, USA
| | - B L Farmer
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, Ohio 45433, USA and Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27606, USA
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Abstract
Amyloid fibrils are structures consisting of many proteins with a well-defined conformation. The formation of these fibrils has been the subject of intense research, largely due to their connection to several diseases. We focus here on the computational studies and discuss these from a free-energy point of view. The fibrillogenic properties of many proteins can be predicted and understood by taking the relevant free energies into account in an appropriate way. This is because both the equilibrium and the kinetic properties of the protein system depend on its free-energy landscape. Advanced simulation techniques can be used to understand the relationship between the free-energy landscape of a protein and its three-dimensional structure and propensity to form amyloid fibrils. We give an overview of existing simulation techniques that operate at a molecular level of detail and that are capable of generating relevant free-energy values. The free energies obtained with these methods can be inserted into a statistical-mechanical or kinetic framework to predict mean fibril properties on length scales and time scales that are inaccessible by molecular-scale simulation methods.
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Affiliation(s)
- Maarten G Wolf
- DelftChemTech, Delft University of Technology, Delft, The Netherlands
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Paluszewski M, Hamelryck T, Winter P. Reconstructing protein structure from solvent exposure using tabu search. Algorithms Mol Biol 2006; 1:20. [PMID: 17069644 PMCID: PMC1635054 DOI: 10.1186/1748-7188-1-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2006] [Accepted: 10/27/2006] [Indexed: 11/10/2022] Open
Abstract
Background A new, promising solvent exposure measure, called half-sphere-exposure (HSE), has recently been proposed. Here, we study the reconstruction of a protein's Cα trace solely from structure-derived HSE information. This problem is of relevance for de novo structure prediction using predicted HSE measure. For comparison, we also consider the well-established contact number (CN) measure. We define energy functions based on the HSE- or CN-vectors and minimize them using two conformational search heuristics: Monte Carlo simulation (MCS) and tabu search (TS). While MCS has been the dominant conformational search heuristic in literature, TS has been applied only a few times. To discretize the conformational space, we use lattice models with various complexity. Results The proposed TS heuristic with a novel tabu definition generally performs better than MCS for this problem. Our experiments show that, at least for small proteins (up to 35 amino acids), it is possible to reconstruct the protein backbone solely from the HSE or CN information. In general, the HSE measure leads to better models than the CN measure, as judged by the RMSD and the angle correlation with the native structure. The angle correlation, a measure of structural similarity, evaluates whether equivalent residues in two structures have the same general orientation. Our results indicate that the HSE measure is potentially very useful to represent solvent exposure in protein structure prediction, design and simulation.
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Affiliation(s)
- Martin Paluszewski
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100 Copenhagen, Denmark
| | - Thomas Hamelryck
- Bioinformatics Center, Institute of Molecular Biology, University of Copenhagen, Universitetsparken 15 building 10, 2100 Copenhagen, Denmark
| | - Pawel Winter
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100 Copenhagen, Denmark
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