1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Pan F, Zhao L, Cai S, Tang X, Mehmood A, Alnadari F, Tuersuntuoheti T, Zhou N, Ai X. Prediction and evaluation of the 3D structure of Macadamia integrifolia antimicrobial protein 2 (MiAMP2) and its interaction with palmitoleic acid or oleic acid: An integrated computational approach. Food Chem 2021; 367:130677. [PMID: 34343803 DOI: 10.1016/j.foodchem.2021.130677] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/11/2021] [Accepted: 07/20/2021] [Indexed: 12/13/2022]
Abstract
This study investigated the physicochemical properties and 3D structure of Macadamia integrifolia antimicrobial protein 2 (MiAMP2) and its interaction with palmitoleic acid (POA) or oleic acid (OA) in macadamia oil. The 3D structure of MiAMP2 was constructed for the first time by ab initio modelling using the TrRosetta server. The results showed that MiAMP2 was highly hydrophilic and had seven disulfide bonds and higher α-helix and β-sheet/turn contents. Molecular simulation showed that the hydrophobic pocket of MiAMP2 created a favourable environment for the binding of POA and OA. Free energy landscape and independent gradient model (IGM) analyses revealed that hydrogen bonds and van der Waals forces were the major driving forces stabilizing complexes formed by MiAMP2 and POA or OA. The present study provides a theoretical basis and new insight for the future development and utilization of macadamia nut protein in the food industry.
Collapse
Affiliation(s)
- Fei Pan
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 100048, China
| | - Lei Zhao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 100048, China.
| | - Shengbao Cai
- Faculty of Agriculture and Food, Yunnan Institute of Food Safety, Kunming University of Science and Technology, Kunming 650500, Yunnan, China
| | - Xiaoning Tang
- Faculty of Chemical Engineering, Kunming University of Science and Technology, Kunming 650500, Yunnan, China
| | - Arshad Mehmood
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 100048, China
| | - Fawze Alnadari
- Department of Food Science and Engineering, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Tuohetisayipu Tuersuntuoheti
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 100048, China
| | - Na Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 100048, China
| | - Xin Ai
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 100048, China
| |
Collapse
|
3
|
Moskovitz Y, Yang H. Modelling of noble anaesthetic gases and high hydrostatic pressure effects in lipid bilayers. SOFT MATTER 2015; 11:2125-2138. [PMID: 25612767 DOI: 10.1039/c4sm02667e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Our objective was to study molecular processes that might be responsible for inert gas narcosis and high-pressure nervous syndrome. The classical molecular dynamics trajectories (200 ns) of dioleoylphosphatidylcholine (DOPC) bilayers simulated by the Berger force field were evaluated for water and the atomic distribution of noble gases around DOPC molecules in the pressure range of 1-1000 bar and at a temperature of 310 K. Xenon and argon have been tested as model gases for general anaesthetics, and neon has been investigated for distortions that are potentially responsible for neurological tremors in hyperbaric conditions. The analysis of stacked radial pair distribution functions of DOPC headgroup atoms revealed the explicit solvation potential of the gas molecules, which correlates with their dimensions. The orientational dynamics of water molecules at the biomolecular interface should be considered as an influential factor, while excessive solvation effects appearing in the lumen of membrane-embedded ion channels could be a possible cause of inert gas narcosis. All the noble gases tested exhibit similar order parameter patterns for both DOPC acyl chains, which are opposite of the patterns found for the order parameter curve at high hydrostatic pressures in intact bilayers. This finding supports the 'critical volume' hypothesis of anaesthesia pressure reversal. The irregular lipid headgroup-water boundary observed in DOPC bilayers saturated with neon in the pressure range of 1-100 bar could be associated with the possible manifestation of neurological tremors at the atomic scale. The non-immobiliser neon also demonstrated the highest momentum impact on the normal component of the DOPC diffusion coefficient representing the monolayer undulation rate, which indicates that enhanced diffusivity rather than atomic size is the key factor.
Collapse
Affiliation(s)
- Yevgeny Moskovitz
- Department of Chemistry, Middle Tennessee State University, Murfreesboro, TN 37130, USA
| | | |
Collapse
|
4
|
Moskovitz Y, Srebnik S. Conformational changes of globular proteins upon adsorption on a hydrophobic surface. Phys Chem Chem Phys 2014; 16:11698-707. [DOI: 10.1039/c4cp00354c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coarse-grained Monte Carlo simulations are used to study thermal denaturation of small globular proteins adsorbed on a hydrophobic surface. Though helices are more stable than sheets, they are highly deformed in the adsorbed protein.
Collapse
Affiliation(s)
- Yevgeny Moskovitz
- Department of Chemistry
- Scientific Computing Research Unit
- University of Cape Town
- Rondebosch 7701, South Africa
| | - Simcha Srebnik
- Department of Chemical Engineering
- Technion – Israel Institute of Technology
- Haifa 32000, Israel
| |
Collapse
|
5
|
Pandey RB, Farmer BL. Random coil to globular thermal response of a protein (H3.1) with three knowledge-based coarse-grained potentials. PLoS One 2012; 7:e49352. [PMID: 23166645 PMCID: PMC3498164 DOI: 10.1371/journal.pone.0049352] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/10/2012] [Indexed: 11/19/2022] Open
Abstract
The effect of temperature on the conformation of a histone (H3.1) is studied by a coarse-grained Monte Carlo simulation based on three knowledge-based contact potentials (MJ, BT, BFKV). Despite unique energy and mobility profiles of its residues, the histone H3.1 undergoes a systematic (possibly continuous) structural transition from a random coil to a globular conformation on reducing the temperature. The range over which such a systematic response in variation of the radius of gyration (R(g)) with the temperature (T) occurs, however, depends on the potential, i.e. ΔT(MJ) ≈ 0.013-0.020, ΔT(BT) ≈ 0.018-0.026, and ΔT(BFKV) ≈ 0.006-0.013 (in reduced unit). Unlike MJ and BT potentials, results from the BFKV potential show an anomaly where the magnitude of R(g) decreases on raising the temperature in a range ΔT(A) ≈ 0.015-0.018 before reaching its steady-state random coil configuration. Scaling of the structure factor, S(q) ∝ q(-1/ν), with the wave vector, q=2π/λ, and the wavelength, λ, reveals a systematic change in the effective dimension (D(e)∼1/ν) of the histone with all potentials (MJ, BT, BFKV): D(e)∼3 in the globular structure with D(e)∼2 for the random coil. Reproducibility of the general yet unique (monotonic) structural transition of the protein H3.1 with the temperature (in contrast to non-monotonic structural response of a similar but different protein H2AX) with three interaction sets shows that the knowledge-based contact potential is viable tool to investigate structural response of proteins. Caution should be exercise with the quantitative comparisons due to differences in transition regimes with these interactions.
Collapse
Affiliation(s)
- Ras B Pandey
- Department of Physics and Astronomy, University of Southern Mississippi, Hattiesburg, Missouri, USA.
| | | |
Collapse
|