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Multiple Antimicrobial Effects of Hybrid Peptides Synthesized Based on the Sequence of Ribosomal S1 Protein from Staphylococcus aureus. Int J Mol Sci 2022; 23:ijms23010524. [PMID: 35008951 PMCID: PMC8745237 DOI: 10.3390/ijms23010524] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/21/2021] [Accepted: 01/01/2022] [Indexed: 02/06/2023] Open
Abstract
The need to develop new antimicrobial peptides is due to the high resistance of pathogenic bacteria to traditional antibiotics now and in the future. The creation of synthetic peptide constructs is a common and successful approach to the development of new antimicrobial peptides. In this work, we use a simple, flexible, and scalable technique to create hybrid antimicrobial peptides containing amyloidogenic regions of the ribosomal S1 protein from Staphylococcus aureus. While the cell-penetrating peptide allows the peptide to enter the bacterial cell, the amyloidogenic site provides an antimicrobial effect by coaggregating with functional bacterial proteins. We have demonstrated the antimicrobial effects of the R23F, R23DI, and R23EI hybrid peptides against Staphylococcus aureus, methicillin-resistant S. aureus (MRSA), Pseudomonas aeruginosa, Escherichia coli, and Bacillus cereus. R23F, R23DI, and R23EI can be used as antimicrobial peptides against Gram-positive and Gram-negative bacteria resistant to traditional antibiotics.
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2
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Salt-dependent elution of uncharged aromatic solutes in ion-exchange chromatography. J Chromatogr A 2018; 1546:46-55. [DOI: 10.1016/j.chroma.2018.02.049] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/15/2018] [Accepted: 02/23/2018] [Indexed: 01/22/2023]
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3
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Hirano A, Maruyama T, Shiraki K, Arakawa T, Kameda T. A study of the small-molecule system used to investigate the effect of arginine on antibody elution in hydrophobic charge-induction chromatography. Protein Expr Purif 2017; 129:44-52. [DOI: 10.1016/j.pep.2016.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 08/24/2016] [Accepted: 09/09/2016] [Indexed: 01/25/2023]
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4
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Hirano A, Arakawa T, Kameda T. Effects of arginine on multimodal anion exchange chromatography. Protein Expr Purif 2015. [DOI: 10.1016/j.pep.2015.07.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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5
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Hirano A, Arakawa T, Kameda T. Interaction of arginine with Capto MMC in multimodal chromatography. J Chromatogr A 2014; 1338:58-66. [DOI: 10.1016/j.chroma.2014.02.053] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 02/18/2014] [Accepted: 02/18/2014] [Indexed: 12/01/2022]
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6
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Free-Energy Landscape of Intrinsically Disordered Proteins Investigated by All-Atom Multicanonical Molecular Dynamics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 805:331-51. [DOI: 10.1007/978-3-319-02970-2_14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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7
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Hirano A, Kameda T, Shinozaki D, Arakawa T, Shiraki K. Molecular Dynamics Simulation of the Arginine-Assisted Solubilization of Caffeic Acid: Intervention in the Interaction. J Phys Chem B 2013; 117:7518-27. [DOI: 10.1021/jp401609p] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Atsushi Hirano
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8562, Japan
| | - Tomoshi Kameda
- Computational Biology Research
Center (CBRC), Advanced Industrial Science and Technology (AIST), Koto, Tokyo 135-0064, Japan
| | - Daisuke Shinozaki
- Institute of Applied Physics, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| | - Tsutomu Arakawa
- Alliance Protein Laboratories, San Diego, California 92121, United States
| | - Kentaro Shiraki
- Institute of Applied Physics, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
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8
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Higo J, Ikebe J, Kamiya N, Nakamura H. Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes. Biophys Rev 2012; 4:27-44. [PMID: 22347892 PMCID: PMC3271212 DOI: 10.1007/s12551-011-0063-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 11/23/2011] [Indexed: 11/29/2022] Open
Abstract
Protein folding and protein-ligand docking have long persisted as important subjects in biophysics. Using multicanonical molecular dynamics (McMD) simulations with realistic expressions, i.e., all-atom protein models and an explicit solvent, free-energy landscapes have been computed for several systems, such as the folding of peptides/proteins composed of a few amino acids up to nearly 60 amino-acid residues, protein-ligand interactions, and coupled folding and binding of intrinsically disordered proteins. Recent progress in conformational sampling and its applications to biophysical systems are reviewed in this report, including descriptions of several outstanding studies. In addition, an algorithm and detailed procedures used for multicanonical sampling are presented along with the methodology of adaptive umbrella sampling. Both methods control the simulation so that low-probability regions along a reaction coordinate are sampled frequently. The reaction coordinate is the potential energy for multicanonical sampling and is a structural identifier for adaptive umbrella sampling. One might imagine that this probability control invariably enhances conformational transitions among distinct stable states, but this study examines the enhanced conformational sampling of a simple system and shows that reasonably well-controlled sampling slows the transitions. This slowing is induced by a rapid change of entropy along the reaction coordinate. We then provide a recipe to speed up the sampling by loosening the rapid change of entropy. Finally, we report all-atom McMD simulation results of various biophysical systems in an explicit solvent.
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Affiliation(s)
- Junichi Higo
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 Japan
| | - Jinzen Ikebe
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 Japan
| | - Narutoshi Kamiya
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 Japan
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9
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Ikeda K, Kameda T, Harada E, Akutsu H, Fujiwara T. Combined Use of Replica-Exchange Molecular Dynamics and Magic-Angle-Spinning Solid-State NMR Spectral Simulations for Determining the Structure and Orientation of Membrane-Bound Peptide. J Phys Chem B 2011; 115:9327-36. [DOI: 10.1021/jp205290t] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Keisuke Ikeda
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871 Japan
| | - Tomoshi Kameda
- Computational Biology Research Center, Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Erisa Harada
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871 Japan
| | - Hideo Akutsu
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871 Japan
| | - Toshimichi Fujiwara
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871 Japan
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10
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Ikebe J, Standley DM, Nakamura H, Higo J. Ab initio simulation of a 57-residue protein in explicit solvent reproduces the native conformation in the lowest free-energy cluster. Protein Sci 2011; 20:187-96. [PMID: 21082745 DOI: 10.1002/pro.553] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
An enhanced conformational sampling method, multicanonical molecular dynamics (McMD), was applied to the ab intio folding of the 57-residue first repeat of human glutamyl- prolyl-tRNA synthetase (EPRS-R1) in explicit solvent. The simulation started from a fully extended structure of EPRS-R1 and did not utilize prior structural knowledge. A canonical ensemble, which is a conformational ensemble thermodynamically probable at an arbitrary temperature, was constructed by reweighting the sampled structures. Conformational clusters were obtained from the canonical ensemble at 300 K, and the largest cluster (i.e., the lowest free-energy cluster), which contained 34% of the structures in the ensemble, was characterized by the highest similarity to the NMR structure relative to all alternative clusters. This lowest free-energy cluster included native-like structures composed of two anti-parallel α-helices. The canonical ensemble at 300 K also showed that a short Gly-containing segment, which adopts an α-helix in the native structure, has a tendency to be structurally disordered. Atomic-level analyses demonstrated clearly that inter-residue hydrophobic interactions drive the helix formation of the Gly-containing segment, and that increasing the hydrophobic contacts accompanies exclusion of water molecules from the vicinity of this segment. This study has shown, for the first time, that the free-energy landscape of a structurally well-ordered protein of about 60 residues is obtainable with an all atom model in explicit water without prior structural knowledge.
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Affiliation(s)
- Jinzen Ikebe
- Graduate School of Frontier Biosciences, Osaka University, Open Laboratories for Advanced Bioscience and Biotechnology, Suita, Osaka 565-0874, Japan
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11
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Hirano A, Kameda T, Arakawa T, Shiraki K. Arginine-Assisted Solubilization System for Drug Substances: Solubility Experiment and Simulation. J Phys Chem B 2010; 114:13455-62. [DOI: 10.1021/jp101909a] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Atsushi Hirano
- Institute of Applied Physics, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan, Computational Biology Research Center, Advanced Industrial Science and Technology, Koto, Tokyo 135-0064, Japan, and Alliance Protein Laboratories, Thousand Oaks, California 91360, United States
| | - Tomoshi Kameda
- Institute of Applied Physics, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan, Computational Biology Research Center, Advanced Industrial Science and Technology, Koto, Tokyo 135-0064, Japan, and Alliance Protein Laboratories, Thousand Oaks, California 91360, United States
| | - Tsutomu Arakawa
- Institute of Applied Physics, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan, Computational Biology Research Center, Advanced Industrial Science and Technology, Koto, Tokyo 135-0064, Japan, and Alliance Protein Laboratories, Thousand Oaks, California 91360, United States
| | - Kentaro Shiraki
- Institute of Applied Physics, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan, Computational Biology Research Center, Advanced Industrial Science and Technology, Koto, Tokyo 135-0064, Japan, and Alliance Protein Laboratories, Thousand Oaks, California 91360, United States
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12
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Umezawa K, Ikebe J, Nomizu M, Nakamura H, Higo J. Conformational requirement on peptides to exert laminin's activities and search for protein segments with laminin's activities. Biopolymers 2009; 92:124-31. [PMID: 19180521 DOI: 10.1002/bip.21148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The human laminin alpha3 chain LG4 module has biological activities of cell adhesion, heparin binding, migration, and neurite outgrowth. The authors had previously identified that the active site of this protein is in residues 1411-1429 (amino-acid sequence = KNSFMALYLSKGRLVFALG called A3G756) and that a three-amino-acid sequence KGR in A3G756 is crucial for exerting the activities. An experiment has shown that a cyclo-hEF3A peptide (a cyclic analog of A3G756) exhibits stronger activities than a linear-hEF3A peptide (a linearized peptide of the cyclo-hEF3A peptide). This experiment implies that adopting a loop conformation may be important for exerting the activities. In this study, the authors first computed the solution structures of the cyclo-hEF3A and linear-hEF3A peptides by molecular dynamics simulations. The obtained conformational ensembles consisted of a variety of conformations, which is a usual property of short peptides in solution. The ensembles involved a fraction where the peptide adopted beta-hairpins and KGR was located at the hairpin head. If there are protein segments that adopt beta-hairpins similar to those sampled from the simulation and have the KGR sequence at the hairpin head, these segments may have some activities. Then, the authors searched a database for segments satisfying these requirements and detected six functional segments. Three of them had laminin's activity, and the remaining three had activities similar to laminin's activities. Analyses on the conformational ensembles of cyclo- and linear-hEF3A peptides suggest that not only the KGR position in the hairpin but also the inter-strand packing is important for exerting laminin's activities.
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Affiliation(s)
- Koji Umezawa
- Graduate School of Frontier Biosciences, Osaka University, Open Laboratories for Advanced Bioscience and Biotechnology, Suita, Osaka, Japan
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13
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Cheluvaraja S, Meirovitch H. Stability of the Free and Bound Microstates of a Mobile Loop of α-Amylase Obtained from the Absolute Entropy and Free Energy. J Chem Theory Comput 2007; 4:192-208. [DOI: 10.1021/ct700116n] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Srinath Cheluvaraja
- Department of Computational Biology, University of Pittsburgh School of Medicine, 3059 BST3, Pittsburgh, Pennsylvania 15260
| | - Hagai Meirovitch
- Department of Computational Biology, University of Pittsburgh School of Medicine, 3059 BST3, Pittsburgh, Pennsylvania 15260
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14
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Ikebe J, Kamiya N, Ito JI, Shindo H, Higo J. Simulation study on the disordered state of an Alzheimer's beta amyloid peptide Abeta(12 36) in water consisting of random-structural, beta-structural, and helical clusters. Protein Sci 2007; 16:1596-608. [PMID: 17656579 PMCID: PMC2203368 DOI: 10.1110/ps.062721907] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The monomeric Alzheimer's beta amyloid peptide, Abeta, is known to adopt a disordered state in water at room temperature, and a circular dichroism (CD) spectroscopy experiment has provided the secondary-structure contents for the disordered state: 70% random, 25% beta-structural, and 5% helical. We performed an enhanced conformational sampling (multicanonical molecular dynamics simulation) of a 25-residue segment (residues 12-36) of Abeta in explicit water and obtained the conformational ensemble over a wide temperature range. The secondary-structure contents calculated from the conformational ensemble at 300 degrees K reproduced the experimental secondary-structure contents. The constructed free-energy landscape at 300 degrees K was not plain but rugged with five clearly distinguishable clusters, and each cluster had its own characteristic tertiary structure: a helix-structural cluster, two beta-structural clusters, and two random-structural clusters. This indicates that the contribution from the five individual clusters determines the secondary-structure contents experimentally measured. The helical cluster had a similarity with a stable helical structure for monomeric Abeta in 2,2,2-trifluoroethanol (TFE)/water determined by an NMR experiment: The positions of helices in the helical cluster were the same as those in the NMR structure, and the residue-residue contact patterns were also similar with those of the NMR structure. The cluster-cluster separation in the conformational space indicates that free-energy barriers separate the clusters at 300 degrees K. The two beta-structural clusters were characterized by different strand-strand hydrogen-bond (H-bond) patterns, suggesting that the free-energy barrier between the two clusters is due to the H-bond rearrangements.
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Affiliation(s)
- Jinzen Ikebe
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
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15
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Kamiya N, Mitomo D, Shea JE, Higo J. Folding of the 25 Residue Aβ(12−36) Peptide in TFE/Water: Temperature-Dependent Transition from a Funneled Free-Energy Landscape to a Rugged One. J Phys Chem B 2007; 111:5351-6. [PMID: 17439167 DOI: 10.1021/jp067075v] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The free-energy landscape of the Alzheimer beta-amyloid peptide Abeta(12-36) in a 40% (v/v) 2,2,2-trifluoroethanol (TFE)/water solution was determined by using multicanonical molecular dynamics simulations. Simulations using this enhanced conformational sampling technique were initiated from a random unfolded polypeptide conformation. Our simulations reliably folded the peptide to the experimental NMR structure, which consists of two linked helices. The shape of the free energy landscape for folding was found to be strongly dependent on temperature: Above 325 K, the overall shape was funnel-like, with the bottom of the funnel coinciding exactly with the NMR structure. Below 325 K, on the other hand, the landscape became increasingly rugged, with the emergence of new conformational clusters connected by low free-energy pathways. Finally, our simulations reveal that water and TFE solvate the polypeptide in different ways: The hydrogen bond formation between TFE and Abeta was enhanced with decreasing temperature, while that between water and Abeta was depressed.
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Affiliation(s)
- Narutoshi Kamiya
- Clinical Genome Informatics Center, Kobe University, Graduate School of Medicine, 1-5-6 Minatojima-Minami-machi, Chuo-ku, Kobe 650-0047, Japan
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16
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Kameda T, Takada S. Secondary structure provides a template for the folding of nearby polypeptides. Proc Natl Acad Sci U S A 2006; 103:17765-70. [PMID: 17101976 PMCID: PMC1693821 DOI: 10.1073/pnas.0602632103] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although protein structures are primarily encoded by their sequences, they are also critically dependent on environmental factors such as solvents and interactions with other molecules. Here we investigate how the folding-energy landscape of a short peptide is altered by interactions with another peptide, by performing atomistic replica-exchange molecular dynamics simulations of polyalanines in various environments. We analyzed the free-energy landscapes of Ala7 and Ala8 in isolation, near an alpha-helix template, and near a beta-strand template. The isolated Ala7 and Ala8 at 270 K were mainly in polyproline II helix conformations and in equilibrium between the alpha-helix and polyproline II helix, respectively, in harmony with the experiment. Interestingly, we found remarkably strong secondary-structure "templating"; namely, the alpha-helix template enhanced alpha-helix conformation and the beta-strand template induced beta-strand conformation in the simulated Ala8. The alpha-helix template lowered the nearby dielectric constant, which strengthened hydrogen bonds in the simulated Ala8, leading to alpha-helix stabilization. The beta-strand template provided hydrogen bond positions to the simulated Ala8, sharply inducing beta-strand structure. With or without templates, the energy landscape of Ala8 is always funnel-like and centered at the alpha-helix conformation, whereas entropic contribution disfavors the alpha-helix, leading to subtle competition. Secondary-structure templating may play a critical role in protein conformation dynamics in the cellular environment.
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Affiliation(s)
- Tomoshi Kameda
- *Graduate School of Science and Technology, Kobe University, Rokkodai, Nada, Kobe 657-8501, Japan
- Computational Biology Research Center, Advanced Industrial Science and Technology, 2-43 Aomi, Koto, Tokyo 135-0064, Japan; and
| | - Shoji Takada
- *Graduate School of Science and Technology, Kobe University, Rokkodai, Nada, Kobe 657-8501, Japan
- Core Research for Evolutionary Science and Technology, Japan Science and Technology Corp., Rokkodai, Nada, Kobe 657-8501, Japan
- To whom correspondence should be addressed at:
Department of Chemistry, Faculty of Science, Kobe University, Rokkodai, Nada, Kobe 657-8501, Japan. E-mail:
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17
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Cheluvaraja S, Meirovitch H. Calculation of the entropy and free energy of peptides by molecular dynamics simulations using the hypothetical scanning molecular dynamics method. J Chem Phys 2006; 125:24905. [PMID: 16848609 DOI: 10.1063/1.2208608] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Hypothetical scanning (HS) is a method for calculating the absolute entropy S and free energy F from a sample generated by any simulation technique. With this approach each sample configuration is reconstructed with the help of transition probabilities (TPs) and their product leads to the configuration's probability, hence to the entropy. Recently a new way for calculating the TPs by Monte Carlo (MC) simulations has been suggested, where all system interactions are taken into account. Therefore, this method--called HSMC--is in principle exact where the only approximation is due to insufficient sampling. HSMC has been applied very successfully to liquid argon, TIP3P water, self-avoiding walks on a lattice, and peptides. Because molecular dynamics (MD) is considered to be significantly more efficient than MC for a compact polymer chain, in this paper HSMC is extended to MD simulations as applied to peptides. Like before, we study decaglycine in vacuum but for the first time also a peptide with side chains, (Val)(2)(Gly)(6)(Val)(2). The transition from MC to MD requires implementing essential changes in the reconstruction process of HSMD. Results are calculated for three microstates, helix, extended, and hairpin. HSMD leads to very stable differences in entropy TDeltaS between these microstates with small errors of 0.1-0.2 kcal/mol (T=100 K) for a wide range of calculation parameters with extremely high efficiency. Various aspects of HSMD and plans for future work are discussed.
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Affiliation(s)
- Srinath Cheluvaraja
- Department of Computational Biology, University of Pittsburgh School of Medicine, 3059 BST3, Pittsburgh, PA 15260, USA
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18
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Ishitani R, Shimizu K, Terada T. Evaluation of efficiency of reference potential spatial warping algorithm in conformational sampling of peptides. J Chem Phys 2006; 124:214902. [PMID: 16774437 DOI: 10.1063/1.2200698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Molecular dynamics (MD) simulation using the reference potential spatial warping algorithm (REPSWA) is a promising method for computing the conformational equilibrium of a system with a rugged energy surface. Its effectiveness has previously been demonstrated using only a simplified model system of a hydrocarbon chain omitting nonbonded interaction terms from the potential energy function. To evaluate the applicability of REPSWA MD simulation to more realistic problems, we applied it to small peptide systems in an aqueous environment. Difficulties were encountered, however, forcing us to devise several modifications. We investigated their effectiveness in comparison to conventional constant-temperature and multicanonical MD simulations. We found that the sampling efficiency of the modified REPSWA MD after a careful optimization of its parameters was better than that of the constant-temperature MD and comparable to that of the multicanonical MD in several cases.
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Affiliation(s)
- Ryuichiro Ishitani
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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19
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20
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Fukuda I, Nakamura H. Molecular dynamics sampling scheme realizing multiple distributions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2005; 71:046708. [PMID: 15903819 DOI: 10.1103/physreve.71.046708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2004] [Indexed: 05/02/2023]
Abstract
We present a molecular-dynamics sampling scheme in which any summation of multiple arbitrarily given distributions can be realized deterministically by a certain theoretical guide. Our scheme thus provides a static view of the composition of the distributions, rather than a dynamic view in which some parameter is switched at a certain time in the simulation process. The proposed method induces the orbit to jump automatically among different phase space regions, without the use of any artificial timing parameter. In addition, the proposed method does not require an assumption that the density of states is smooth. We applied it to multiple Tsallis distributions and established a suitable series of parameter values for which the sum of the distributions allows broad sampling. Numerical simulations applied to fundamental models with multi-Tsallis distributions showed efficient sampling, characterized by an energy trajectory that was totally different from that associated with each single distribution.
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Affiliation(s)
- Ikuo Fukuda
- National Institute of Advanced Industrial Science and Technology, 2-41-6, Aomi, Koto-ku, Tokyo 135-0064, Japan
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21
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Ikeda K, Tomii K, Yokomizo T, Mitomo D, Maruyama K, Suzuki S, Higo J. Visualization of conformational distribution of short to medium size segments in globular proteins and identification of local structural motifs. Protein Sci 2005; 14:1253-65. [PMID: 15802651 PMCID: PMC2253271 DOI: 10.1110/ps.04956305] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Analysis of the conformational distribution of polypeptide segments in a conformational space is the first step for understanding a principle of structural diversity of proteins. Here, we present a statistical analysis of protein local structures based on interatomic C(alpha) distances. Using principal component analysis (PCA) on the intrasegment C(alpha)-C(alpha) atomic distances, the conformational space of protein segments, which we call the protein segment universe, has been visualized, and three essential coordinate axes, suitable for describing the universe, have been identified. Three essential axes specified radius of gyration, structural symmetry, and separation of hairpin structures from other structures. Among the segments of arbitrary length, 6-22 residues long, the conservation of those axes was uncovered. Further application of PCA to the two largest clusters in the universe revealed local structural motifs. Although some of motifs have already been reported, we identified a possibly novel strand motif. We also showed that a capping box, which is one of the helix capping motifs, was separated into independent subclusters based on the C(alpha) geometry. Implications of the strand motif, which may play a role for protein-protein interaction, are discussed. The currently proposed method is useful for not only mapping the immense universe of protein structures but also identification of structural motifs.
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Affiliation(s)
- Kazuyoshi Ikeda
- Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
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22
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23
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Ikeda K, Higo J. Free-energy landscape of a chameleon sequence in explicit water and its inherent alpha/beta bifacial property. Protein Sci 2004; 12:2542-8. [PMID: 14573865 PMCID: PMC2366969 DOI: 10.1110/ps.03143803] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A sequence in yeast MATalpha2/MCM1/DNA complex that folds into alpha-helix or beta-hairpin depending on the surroundings has been known as "chameleon" sequence. We obtained the free-energy landscape of this sequence by using a generalized-ensemble method, multicanonical molecular dynamics simulation, to sample the conformational space. The system was expressed with an all-atom model in explicit water, and the initial conformation for the simulation was a random one. The free-energy landscape demonstrated that this sequence inherently has an ability to form either alpha or beta structure: The conformational distribution in the landscape consisted of two alpha-helical clusters with different packing patterns of hydrophobic residues, and four beta-hairpin clusters with different strand-strand interaction patterns. Narrow pathways connecting the clusters were found, and analysis on the pathways showed that a compact structure formed at the N-terminal root of the chameleon sequence controls the cluster-cluster transitions. The free-energy landscape indicates that a small conditional change induces alpha-beta transitions. Additional unfolding simulations done with replacing amino acids showed that the chameleon sequence has an advantage to form an alpha-helix. Current study may be useful to understand the mechanism of diseases resulting from abnormal chain folding, such as amyloid disease.
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Affiliation(s)
- Kazuyoshi Ikeda
- Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan
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Tidow H, Lauber T, Vitzithum K, Sommerhoff CP, Rösch P, Marx UC. The Solution Structure of a Chimeric LEKTI Domain Reveals a Chameleon Sequence. Biochemistry 2004; 43:11238-47. [PMID: 15366933 DOI: 10.1021/bi0492399] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The conversion of an alpha-helical to a beta-strand conformation and the presence of chameleon sequences are fascinating from the perspective that such structural features are implicated in the induction of amyloid-related fatal diseases. In this study, we have determined the solution structure of a chimeric domain (Dom1PI) from the multidomain Kazal-type serine proteinase inhibitor LEKTI using multidimensional NMR spectroscopy. This chimeric protein was constructed to investigate the reasons for differences in the folds of the homologous LEKTI domains 1 and 6 [Lauber, T., et al. (2003) J. Mol. Biol. 328, 205-219]. In Dom1PI, two adjacent phenylalanine residues (F28 and F29) of domain 1 were substituted with proline and isoleucine, respectively, as found in the corresponding P4' and P5' positions of domain 6. The three-dimensional structure of Dom1PI is significantly different from the structure of domain 1 and closely resembles the structure of domain 6, despite the sequence being identical to that of domain 1 except for the two substituted phenylalanine residues and being only 31% identical to the sequence of domain 6. The mutation converted a short 3(10)-helix into an extended loop conformation and parts of the long COOH-terminal alpha-helix of domain 1 into a beta-hairpin structure. The latter conformational change occurs in a sequence stretch distinct from the region containing the substituted residues. Therefore, this switch from an alpha-helical structure to a beta-hairpin structure indicates a chameleon sequence of seven residues. We conclude that the secondary structure of Dom1PI is determined not only by the local protein sequence but also by nonlocal interactions.
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Affiliation(s)
- Henning Tidow
- Lehrstuhl für Biopolymere, Universität Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
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Lindorff-Larsen K, Vendruscolo M, Paci E, Dobson CM. Transition states for protein folding have native topologies despite high structural variability. Nat Struct Mol Biol 2004; 11:443-9. [PMID: 15098020 DOI: 10.1038/nsmb765] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2003] [Accepted: 03/23/2004] [Indexed: 11/09/2022]
Abstract
We present a structural analysis of the folding transition states of three SH3 domains. Our results reveal that the secondary structure is not yet fully formed at this stage of folding and that the solvent is only partially excluded from the interior of the protein. Comparison of the members of the transition state ensemble with a database of native folds shows that, despite substantial local variability, the transition state structures can all be classified as having the topology characteristic of an SH3 domain. Our results suggest a mechanism for folding in which the formation of a network of interactions among a subset of hydrophobic residues ensures that the native topology is generated. Such a mechanism enables high fidelity in folding while minimizing the need to establish a large number of specific interactions in the conformational search.
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Affiliation(s)
- Kresten Lindorff-Larsen
- University of Cambridge, University Chemical Laboratory, Lensfield Road, Cambridge, CB2 1EW, UK
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