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Lee HJ, Liu SW, Sulyok-Eiler M, Harmat V, Farkas V, Bánóczi Z, El Khabchi M, Shawn Fan HJ, Hirao K, Song JW. Neighbor effect on conformational spaces of alanine residue in azapeptides. Heliyon 2024; 10:e33159. [PMID: 39021983 PMCID: PMC11253059 DOI: 10.1016/j.heliyon.2024.e33159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/10/2024] [Accepted: 06/14/2024] [Indexed: 07/20/2024] Open
Abstract
The conformational properties of Alanine (Ala) residue have been investigated to understand protein folding and develop force fields. In this work, we examined the neighbor effect on the conformational spaces of Ala residue using model azapeptides, Ac-Ala-azaGly-NHMe (3, AaG), and Ac-azaGly-Ala-NHMe (4, aGA1). Ramachandran energy maps were generated by scanning (φ, ψ) dihedral angles of the Ala residues in models with the fixed dihedral angles (φ = ±90°, ψ = ±0° or ±180°) of azaGly residue using LCgau-BOP and LCgau-BOP + LRD functionals in the gas and water phases. The integral-equation-formalism polarizable continuum model (IEF-PCM) and a solvation model density (SMD) were employed to mimic the solvation effect. The most favorable conformation of Ala residue in azapeptide models is found as the polyproline II (βP), inverse γ-turn (γ'), β-sheet (βS), right-handed helix (αR), or left-handed helix (αL) depending on the conformation of neighbor azaGly residue in isolated form. Solvation methods exhibit that the Ala residue favors the βP, δR, and αR conformations regardless of its position in azapeptides 3 and 4 in water. Azapeptide 5, Ac-azaGly-Ala-NH2 (aGA2), was synthesized to evaluate the theoretical results. The X-ray structure showed that azaGly residue adopts the polyproline II (βP) and Ala residue adopts the right-handed helical (αR) structure in aGA2. The conformational preferences of aGA2 and the dimer structure of aGA2 based on the X-ray structure were examined to assess the performance of DFT functionals. In addition, the local minima of azapeptide 6, Ac-Phe-azaGly-NH2 (FaG), were compared with the previous experimental results. SMD/LCgau-BOP + LRD methods agreed well with the reported experimental results. The results suggest the importance of weak dispersion interactions, neighbor effect, and solvent influence in the conformational preferences of Ala residue in model azapeptides.
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Affiliation(s)
- Ho-Jin Lee
- Division of Natural and Mathematics Sciences, LeMoyne-Own College, Memphis, TN, 38126, USA
- Department of Natural Sciences, Southwest Tennessee Community College, Memphis, TN, 38015, USA
| | - Shi-Wei Liu
- College of Chemical Engineering, Sichuan University of Science and Engineering, Zigong City, Sichuan Province, 64300, PR China
| | - Máté Sulyok-Eiler
- Laboratory of Structural Biology and Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
- Hevesy György PhD School of Chemistry, Eötvös Loránd University, Budapest, Hungary
| | - Veronika Harmat
- Laboratory of Structural Biology and Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
- HUN-REN - ELTE Protein Modeling Research Group, Budapest, Hungary
| | - Viktor Farkas
- Laboratory of Structural Biology and Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
- HUN-REN - ELTE Protein Modeling Research Group, Budapest, Hungary
| | - Zoltán Bánóczi
- Department of Organic Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, 1117, Budapest, Hungary
- HUN-REN-ELTE Research Group of Peptide Chemistry, 1117, Budapest, Hungary
| | - Mouna El Khabchi
- LIMAS, Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdallah, Fez, Morocco
| | - Hua-Jun Shawn Fan
- College of Chemical Engineering, Sichuan University of Science and Engineering, Zigong City, Sichuan Province, 64300, PR China
| | - Kimihiko Hirao
- Fukui Institute for Fundamental Chemistry, Kyoto University, Takano, Nishihiraki-cho 34-4, Sakyo-ku, Kyoto, 606-8103, Japan
| | - Jong-Won Song
- Department of Chemistry Education, Daegu University, Daegudae-ro 201, Gyeongsan-si, Gyeongsangbuk-do, 38453, Republic of Korea
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2
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Zinovjev K, Hedges L, Montagud Andreu R, Woods C, Tuñón I, van der Kamp MW. emle-engine: A Flexible Electrostatic Machine Learning Embedding Package for Multiscale Molecular Dynamics Simulations. J Chem Theory Comput 2024; 20:4514-4522. [PMID: 38804055 PMCID: PMC11171281 DOI: 10.1021/acs.jctc.4c00248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 05/29/2024]
Abstract
We present in this work the emle-engine package (https://github.com/chemle/emle-engine)─the implementation of a new machine learning embedding scheme for hybrid machine learning potential/molecular-mechanics (ML/MM) dynamics simulations. The package is based on an embedding scheme that uses a physics-based model of the electronic density and induction with a handful of tunable parameters derived from in vacuo properties of the subsystem to be embedded. This scheme is completely independent of the in vacuo potential and requires only the positions of the atoms of the machine learning subsystem and the positions and partial charges of the molecular mechanics environment. These characteristics allow emle-engine to be employed in existing QM/MM software. We demonstrate that the implemented electrostatic machine learning embedding scheme (named EMLE) is stable in enhanced sampling molecular dynamics simulations. Through the calculation of free energy surfaces of alanine dipeptide in water with two different ML options for the in vacuo potential and three embedding models, we test the performance of EMLE. When compared to the reference DFT/MM surface, the EMLE embedding is clearly superior to the MM one based on fixed partial charges. The configurational dependence of the electronic density and the inclusion of the induction energy introduced by the EMLE model leads to a systematic reduction in the average error of the free energy surface when compared to MM embedding. By enabling the usage of EMLE embedding in practical ML/MM simulations, emle-engine will make it possible to accurately model systems and processes that feature significant variations in the charge distribution of the ML subsystem and/or the interacting environment.
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Affiliation(s)
- Kirill Zinovjev
- Departamento
de Química Física, Universidad
de Valencia, 46100 Burjassot, Spain
| | - Lester Hedges
- School
of Biochemistry, University of Bristol, Biomedical Sciences Building, University
Walk, Bristol BS8 1TD, U.K.
- Research
Software Engineering, Advanced Computing
Research Centre, 31 Great
George Street, Bristol BS1 5QD, U.K.
| | | | - Christopher Woods
- Research
Software Engineering, Advanced Computing
Research Centre, 31 Great
George Street, Bristol BS1 5QD, U.K.
| | - Iñaki Tuñón
- Departamento
de Química Física, Universidad
de Valencia, 46100 Burjassot, Spain
| | - Marc W. van der Kamp
- School
of Biochemistry, University of Bristol, Biomedical Sciences Building, University
Walk, Bristol BS8 1TD, U.K.
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3
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Adasme-Carreño F, Ochoa-Calle A, Galván M, Ireta J. Conformational preference of dipeptide zwitterions in aqueous solvents. Phys Chem Chem Phys 2024; 26:8210-8218. [PMID: 38384231 DOI: 10.1039/d3cp05742a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Proper description of solvent effects is challenging for theoretical methods, particularly if the solute is a zwitterion. Here, a series of theoretical procedures are used to determine the preferred solvated conformations of twelve hydrophobic dipeptides (Leu-Leu, Leu-Phe, Phe-Leu, Ile-Leu, Phe-Phe, Ala-Val, Val-Ala, Ala-Ile, Ile-Ala, Ile-Val, Val-Ile and Val-Val) in the zwitterionic state. First, the accuracy of density functional theory (DFT), combined with different implicit solvent models, for describing zwitterions in aqueous solvent is assessed by comparing the predicted against the experimental glycine tautomerization energy, i.e., the energetic difference between canonical and zwitterionic glycine in aqueous solvents. It is found that among the tested solvation schemes, the charge-asymmetric nonlocally determined local-electric solvation model (CANDLE) predicts an energetic difference in excellent agreement with the experimental value. Next, DFT-CANDLE is used to determine the most favorable solvated conformation for each of the investigated dipeptide zwitterions. The CANDLE-solvated structures are obtained by exploring the conformational space of each dipeptide zwitterion concatenating DFT calculations, in vacuum, with classical molecular dynamics simulations, in explicit solvents, and DFT calculations including explicit water molecules. It is found that the energetically most favorable conformations are similar to those of the dipeptide zwitterions in their respective crystal structures. Such structural agreement is indicative of the DFT-CANDLE accomplishment of the description of solvated zwitterions, and suggests that these biomolecules self-assemble as quasi-rigid objects.
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Affiliation(s)
- Francisco Adasme-Carreño
- Centro de Investigación de Estudios Avanzados del Maule (CIEAM), Vicerrectorá de Investigación y Postgrado Universidad Católica del Maule, Talca 3480112, Chile.
- Laboratorio de Bioinformática y Química Computacional (LBQC), Departamento de Medicina Traslacional, Facultad de Medicina, Universidad Católica del Maule, Talca 3480112, Chile
| | - Alvaro Ochoa-Calle
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de México 09340, Mexico.
| | - Marcelo Galván
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de México 09340, Mexico.
| | - Joel Ireta
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de México 09340, Mexico.
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4
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Yuan Y, Wang F. Dipole Cooperativity and Polarization Frustration Determine the Secondary Structure Distribution of Short Alanine Peptides in Water. J Phys Chem B 2023; 127:3126-3138. [PMID: 36848625 PMCID: PMC10108861 DOI: 10.1021/acs.jpcb.2c07947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/16/2023] [Indexed: 03/01/2023]
Abstract
The physical driving forces for secondary structure preferences of hydrated alanine peptide are investigated with B3LYP-D3(BJ) and the adaptive force matching (AFM) method. The AFM fit to the DFT surface, ALA2022, provides excellent agreement with the nuclear magnetic resonance scalar coupling constants from experiments. In turn, the model is used to gain insight into the physical driving forces behind secondary structure preferences of hydrated peptides. DFT calculations with and without the Conductor-like Screening Model (COSMO) show that the α helix is stabilized by solvent polarization due to dipole cooperativity. The two adjacent amide groups in β strand form a near-planar trapezoid that is not much larger than the size of water molecules. When the finite size of a water molecule is considered, the stabilization from solvent polarization for such a trapezoid is frustrated. Water molecules cannot find orientations to properly stabilize all four polar regions close to each other with such an awkward arrangement. This leads to quite substantial reduction in polarization stabilization. Although the polyproline II (PP-II) conformation is very similar to the β strand, the small twist in the backbone angles allowed much improved polarization stabilization. The improved polarization, when combined with favorable intrapeptide interactions, leads to the PP-II to be lowest in free energy. Other factors, such as the entropic TΔS and the ϕ, ψ coupling terms, are also studied but are found to play only a minor role. The insight shown in this work helps to better understand the structure of globular and intrinsic disordered proteins and facilitate future force field development.
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Affiliation(s)
- Ying Yuan
- Department of Chemistry and
Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Feng Wang
- Department of Chemistry and
Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
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5
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Zhang S, Sun L, Dong L, Bao Z, Lin S. Targeted regulation of pulsed electric field (PEF) treatment on responsive amino acids based on the molecular dynamic simulation. INNOV FOOD SCI EMERG 2022. [DOI: 10.1016/j.ifset.2022.103197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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6
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Chakraborty D, Banerjee A, Wales DJ. Side-Chain Polarity Modulates the Intrinsic Conformational Landscape of Model Dipeptides. J Phys Chem B 2021; 125:5809-5822. [PMID: 34037392 PMCID: PMC8279551 DOI: 10.1021/acs.jpcb.1c02412] [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: 11/29/2022]
Abstract
![]()
The
intrinsic conformational preferences of small peptides may
provide additional insight into the thermodynamics and kinetics of
protein folding. In this study, we explore the underlying energy landscapes
of two model peptides, namely, Ac-Ala-NH2 and Ac-Ser-NH2, using geometry-optimization-based tools developed within
the context of energy landscape theory. We analyze not only how side-chain
polarity influences the structural preferences of the dipeptides,
but also other emergent properties of the landscape, including heat
capacity profiles, and kinetics of conformational rearrangements.
The contrasting topographies of the free energy landscape agree with
recent results from Fourier transform microwave spectroscopy experiments,
where Ac-Ala-NH2 was found to exist as a mixture of two
conformers, while Ac-Ser-NH2 remained structurally locked,
despite exhibiting an apparently rich conformational landscape.
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Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, 24th Street Stop A5300, Austin, Texas 78712, United States
| | - Atreyee Banerjee
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.,Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - David J Wales
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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7
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Diaz DB, Appavoo SD, Bogdanchikova AF, Lebedev Y, McTiernan TJ, Dos Passos Gomes G, Yudin AK. Illuminating the dark conformational space of macrocycles using dominant rotors. Nat Chem 2021; 13:218-225. [PMID: 33589789 DOI: 10.1038/s41557-020-00620-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023]
Abstract
Three-dimensional conformation is the primary determinant of molecular properties. The thermal energy available at room temperature typically equilibrates the accessible conformational states. Here, we introduce a method for isolating unique and previously understudied conformations of macrocycles. The observation of unusual conformations of 16- to 22-membered rings has been made possible by controlling their interconversion using dominant rotors, which represent tunable atropisomeric constituents with relatively high rotational barriers. Density functional theory and in situ NMR measurements suggest that dominant rotor candidates for the amino-acid-based structures considered here should possess a rotational energy barrier of at least 25 kcal mol-1. Notable differences in the geometries of the macrocycle conformations were identified by NMR spectroscopy and X-ray crystallography. There is evidence that amino acid residues can be forced into rare turn motifs not observed in the corresponding linear counterparts and homodetic rings. These findings should unlock new avenues for studying the conformation-activity relationships of bioactive molecules.
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Affiliation(s)
- Diego B Diaz
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Solomon D Appavoo
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | | | - Yury Lebedev
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | | | - Gabriel Dos Passos Gomes
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Andrei K Yudin
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.
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8
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Lake PT, Mattson MA, McCullagh M. Implicit Solvation Using the Superposition Approximation (IS-SPA): Extension to Peptides in a Polar Solvent. J Chem Theory Comput 2021; 17:703-713. [PMID: 33428425 DOI: 10.1021/acs.jctc.0c01094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Efficient, accurate, and adaptable implicit solvent models remain a significant challenge in the field of molecular simulation. A recent implicit solvent model, IS-SPA, based on approximating the mean solvent force using the superposition approximation, provides a platform to achieve these goals. IS-SPA was originally developed to handle nonpolar solutes in a polar solvent and did not accurately capture polar solvation. Here, we demonstrate that IS-SPA can accurately capture polar solvation by incorporating solvent orientation and accounting for the contributions from long ranged electrostatics. Solvent orientation is approximated as that of an ideal dipole aligned in a mean electrostatic field and an analytic form of the long ranged electrostatics is derived. Parameters for the model are calculated from explicit solvent simulations of an isolated atom or molecule and include atom-based solvent densities, mean electric field functions, radially symmetric averaged Lennard-Jones forces, and multipoles of the explicit solvent model. Using these parameters, IS-SPA accounts for asymmetry of charge solvation and reproduces the explicit solvent potential of mean force of dimerization of two oppositely charged Lennard-Jones spheres in chloroform with high fidelity. Additionally, the model more accurately captures the effect of explicit solvent on the monomer and dimer configurations of alanine dipeptide in chloroform than a generalized Born or constant density dielectric model. The current version of the algorithm is expected to outperform explicit solvent simulations for aggregation of small peptides at concentrations below 150 mM, well above the typical experimental concentrations for these materials.
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Affiliation(s)
- Peter T Lake
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078-1010, United States
| | - Max A Mattson
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872, United States
| | - Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078-1010, United States
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9
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On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides. Polymers (Basel) 2020; 13:polym13010099. [PMID: 33383731 PMCID: PMC7795291 DOI: 10.3390/polym13010099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 12/02/2022] Open
Abstract
Solvent pH is an important property that defines the protonation state of the amino acids and, therefore, modulates the interactions and the conformational space of the biochemical systems. Generally, this thermodynamic variable is poorly considered in Molecular Dynamics (MD) simulations. Fortunately, this lack has been overcome by means of the Constant pH Molecular Dynamics (CPHMD) methods in the recent decades. Several studies have reported promising results from these approaches that include pH in simulations but focus on the prediction of the effective pKa of the amino acids. In this work, we want to shed some light on the CPHMD method and its implementation in the AMBER suitcase from a conformational point of view. To achieve this goal, we performed CPHMD and conventional MD (CMD) simulations of six protonatable amino acids in a blocked tripeptide structure to compare the conformational sampling and energy distributions of both methods. The results reveal strengths and weaknesses of the CPHMD method in the implementation of AMBER18 version. The change of the protonation state according to the chemical environment is presumably an improvement in the accuracy of the simulations. However, the simulations of the deprotonated forms are not consistent, which is related to an inaccurate assignment of the partial charges of the backbone atoms in the CPHMD residues. Therefore, we recommend the CPHMD methods of AMBER program but pointing out the need to compare structural properties with experimental data to bring reliability to the conformational sampling of the simulations.
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10
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Tyagi C, Marik T, Szekeres A, Vágvölgyi C, Kredics L, Ötvös F. Tripleurin XIIc: Peptide Folding Dynamics in Aqueous and Hydrophobic Environment Mimic Using Accelerated Molecular Dynamics. Molecules 2019; 24:E358. [PMID: 30669493 PMCID: PMC6359335 DOI: 10.3390/molecules24020358] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 01/14/2019] [Accepted: 01/18/2019] [Indexed: 01/11/2023] Open
Abstract
Peptaibols are a special class of fungal peptides with an acetylated N-terminus and a C-terminal 1,2-amino alcohol along with non-standard amino acid residues. New peptaibols named tripleurins were recently identified from a strain of the filamentous fungal species Trichoderma pleuroti, which is known to cause green mould disease on cultivated oyster mushrooms. To understand the mode of action of these peptaibols, the three-dimensional structure of tripleurin (TPN) XIIc, an 18-mer peptide, was elucidated using an enhanced sampling method, accelerated MD, in water and chloroform solvents. Non-standard residues were parameterized by the Restrained Electrostatic Potential (RESP) charge fitting method. The dihedral distribution indicated towards a right-handed helical formation for TPN XIIc in both solvents. Dihedral angle based principal component analysis revealed a propensity for a slightly bent, helical folded conformation in water solvent, while two distinct conformations were revealed in chloroform: One that folds into highly bent helical structure that resembles a beta-hairpin and another with an almost straight peptide backbone appearing as a rare energy barrier crossing event. The hinge-like movement of the terminals was also observed and is speculated to be functionally relevant. The convergence and efficient sampling is addressed using Cartesian PCA and Kullback-Leibler divergence methods.
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Affiliation(s)
- Chetna Tyagi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
| | - Tamás Marik
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
| | - András Szekeres
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
| | - Ferenc Ötvös
- Institute of Biochemistry, Biological Research Centre, Szeged, Temesvári krt. 62, H-6726 Szeged, Hungary.
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11
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Zhu Q, Yuan Y, Ma J, Dong H. A Data‐Driven Accelerated Sampling Method for Searching Functional States of Proteins. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201800171] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Qiang Zhu
- Key Laboratory of Mesoscopic Chemistry of Ministry of EducationInstitute of Theoretical and Computational Chemistry School of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P. R. China
- Kuang Yaming Honors SchoolNanjing University Nanjing 210023 P. R. China
| | - Yigao Yuan
- Kuang Yaming Honors SchoolNanjing University Nanjing 210023 P. R. China
| | - Jing Ma
- Key Laboratory of Mesoscopic Chemistry of Ministry of EducationInstitute of Theoretical and Computational Chemistry School of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P. R. China
| | - Hao Dong
- Kuang Yaming Honors SchoolNanjing University Nanjing 210023 P. R. China
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12
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Tasharrofi S, Taghdisian H, Golchoobi A. Vertically aligned double wall carbon nanotube arrays adsorbent for pure and mixture adsorption of H 2S, ethylbenzene and carbon monoxide, grand canonical Monte Carlo simulation. J Mol Graph Model 2018; 81:86-96. [PMID: 29547876 DOI: 10.1016/j.jmgm.2018.02.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/25/2018] [Accepted: 02/18/2018] [Indexed: 12/17/2022]
Abstract
In this study, pure and ternary adsorption of hydrogen sulfide (H2S), ethylbenzene (EB), and carbon monoxide (CO) on different arrays of zigzag double wall carbon nanotube was investigated using grand canonical Monte Carlo simulations. The internal diameters of nanotube were fixed at 2r = 50.17 Å while nanotube wall distances were different values from d = 0 Å to d = 150 Å. Pure simulation results indicated that adsorption quantity of H2S and EB in low pressure ranges of P = 1.9 bar to P = 3.1 bar was at least 100% more than CO adsorption quantities. At high pressure ranges of P = 23.1 bar to P = 38.2 bar H2S adsorption was greater than EB and CO by about 200 molecules per unit cell (UC) at low nanotube distances. This was related to smaller kinetic diameter and greater dipole moment of H2S compared to EB and CO. At higher nanotube distance the effect of size however disappears and all three gases approach to adsorption quantity of about 800 molecules/UC. Graphical representation of adsorption areas showed that H2S and CO form multilayer adsorption around nanotube inner and outer walls while EB fill the whole space uniformly without any congestion around the walls. Ternary adsorption results EB/CO and H2S/CO selectivity are greater than EB/H2S selectivity. In addition, at smaller nanotube distances H2S/CO selectivity is generally higher than EB/CO selectivity, which at higher nanotube distance the order becomes revers suggesting that size dependent effects on adsorption vanishes. Isosteric heat of adsorption shows that the order of EB > H2S > CO suggesting that ethylbenzene interaction with nanotube arrays was strongest. Although H2S has a greater dipole moment and smaller molecular dimension, EB adsorption at higher nanotube distance is greater than H2S by at least 50% probably because EB is less volatile.
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Affiliation(s)
- Saeideh Tasharrofi
- Research Institute of Petroleum Industry(RIPI), West Side of Azadi Complex, Tehran, 1485733111, Iran.
| | - Hossein Taghdisian
- Research Institute of Petroleum Industry(RIPI), West Side of Azadi Complex, Tehran, 1485733111, Iran.
| | - Abdollah Golchoobi
- Research Institute of Petroleum Industry(RIPI), West Side of Azadi Complex, Tehran, 1485733111, Iran.
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