1
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Zhao J, Yu P, Dong T, Wu Y, Yang F, Wang J. Chasing weakly-bound biological water in aqueous environment near the peptide backbone by ultrafast 2D infrared spectroscopy. Commun Chem 2024; 7:82. [PMID: 38605209 PMCID: PMC11009226 DOI: 10.1038/s42004-024-01170-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 04/05/2024] [Indexed: 04/13/2024] Open
Abstract
There has been a long-standing debate as to how many hydrogen bonds a peptide backbone amide can form in aqueous solution. Hydrogen-bonding structural dynamics of N-ethylpropionamide (a β-peptide model) in water was examined using infrared (IR) spectroscopy. Two amide-I sub bands arise mainly from amide C=O group that forms strong H-bonds with solvent water molecules (SHB state), and minorly from that involving one weak H-bond with water (WHB state). This picture is supported by molecular dynamics simulations and ab-initio calculations. Further, thermodynamics and kinetics of the SHB and WHB species were examined mainly by chemical-exchange two-dimensional IR spectroscopy, yielding an activation energy for the SHB-to-WHB exchange of 13.25 ± 0.52 kJ mol‒1, which occurs in half picosecond at room temperature. Our results provided experimental evidence of an unstable water molecule near peptide backbone, allowing us to gain more insights into the dynamics of the protein backbone hydration.
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Affiliation(s)
- Juan Zhao
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pengyun Yu
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tiantian Dong
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanzhou Wu
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fan Yang
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianping Wang
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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2
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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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3
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Lanza G. Water model for hydrophobic cavities: structure and energy from quantum-chemical calculations. Phys Chem Chem Phys 2023; 25:6902-6913. [PMID: 36799662 DOI: 10.1039/d2cp05195h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
This ab initio study aims to design a series of large water clusters having a hollow clathrate-like cage able to host hydrophobic solutes of various sizes. Starting from the (H2O)n (n = 18, 20, 24 and 28) hollow cages, water layers have been added in a stepwise manner in order to model the configuration of water molecules beyond the primary shell. The large (H2O)100, (H2O)120 and (H2O)140 clusters complete the hydrogen bonding network of the cage with optimal and regular tiling of the do-, tetra-decahedron and hexa-decahedron, respectively. This study is corroborated by an investigation of dense water clusters up to the (H2O)123 one, being highly consistent with experimental data on ice concerning the electronic and zero-point energies for aggregate formation at 0 K and enthalpy and entropy at 273 K. The cavity creation profoundly alters the orientation of water molecules compared with those found in dense clusters. Nevertheless, such a large reorganization is necessary to maximize the water-water attraction by making it similar to the one found in dense clusters. The cage formation is an endothermic process; however, the computed values are large compared with previous reports for hydrocarbon aqueous solutions. Larger clusters are required for a more fruitful comparison.
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Affiliation(s)
- Giuseppe Lanza
- Dipartimento di Scienze del Farmaco e della Salute, Università di Catania, Viale A. Doria 6, Catania, 95125, Italy.
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4
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O'Neill N, Lima TA, Ferreira FF, Thursch L, Alvarez N, Schweitzer-Stenner R. Forbidden Secondary Structures Found in Gel-Forming Fibrils of Glycylphenylalanylglycine. J Phys Chem B 2022; 126:8080-8093. [PMID: 36194765 DOI: 10.1021/acs.jpcb.2c05010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The zwitterionic l-tripeptide glycylphenylalanylglycine self-assembles into very long crystalline fibrils in an aqueous solution, which causes the formation of an exceptionally strong gel phase (G' ∼ 5 × 106 Pa). The Rietveld refinement analysis of its powder X-ray diffraction (PXRD) pattern reveals a unit cell with four peptides forming a P212121 space group and adopting an inverse polyproline II conformation, that is, a right-handed helical structure that occupies the "forbidden" region of the Ramachandran plot. This unusual structure is stabilized by a plethora of intermolecular interactions facilitated by the large number of different functional groups of the unblocked tripeptide. Comparisons of simulated and experimental Fourier transform infrared and vibrational circular dichroism (VCD) amide I' profiles corroborate the PXRD structure. Our experimental setup reduces the sample to a quasi-two-dimensional network of fibrils. We exploited the influence of this reduced dimensionality on the amide I VCD to identify the main fibril axis. We demonstrate that PXRD, vibrational spectroscopy, and amide I simulations provide a powerful toolset for secondary structure and fibril axis determination.
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Affiliation(s)
- Nichole O'Neill
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania19104, United States.,Department of Chemical Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania19104, United States
| | - Thamires A Lima
- Department of Chemical Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania19104, United States
| | - Fabio Furlan Ferreira
- Center for Natural and Human Sciences (CCNH), Federal University of ABC (UFABC), Av. Dos Estados, 5001, S622-3, Santo André, São Paulo09210-580, Brazil
| | - Lavenia Thursch
- Department of Chemical Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania19104, United States
| | - Nicolas Alvarez
- Department of Chemical Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania19104, United States
| | - Reinhard Schweitzer-Stenner
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania19104, United States
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5
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Lanza G, Chiacchio MA. On the size, shape and energetics of the hydration shell around alkanes. Phys Chem Chem Phys 2021; 23:24852-24865. [PMID: 34723301 DOI: 10.1039/d1cp02888j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A large number of clathrate-like cages have been proposed as the very first hydration shell of alkanes. The cages include canonical structures commonly found in clathrate hydrates and many others, not previously reported, derived from the carbon fullerene cavities. These structures have a rich and variegated form, which can adapt to the shape and conformation of the solute. They avoid "wasting" hydrogen bonds, while minimizing the volume cage and maximizing the solute-solvent van der Waals interactions. DFT/M06-2X and MP2 ab initio calculations give comparable structural and energetic results although the latter predicts slightly larger cages for a given solute. It is shown that the van der Waals interactions are substantial and the large exoenergetic values found for isobutane and cyclopentane provide an explanation for the surprising high melting points of related hydrates at room pressure. The encaging enthalpy for various hydrocarbons is similar to the enthalpy of solution measured at a temperature just above the melting point of aqueous hydrocarbon solutions, thus indicating that water molecules should not deviate too much from the configuration with O-H bonds tangentially oriented with respect to the solute surface. The computed trend differs from the enthalpy of solution measured at room temperature, thus the very first hydration shell departs, up to a certain degree, from the clathrate-like structures.
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Affiliation(s)
- Giuseppe Lanza
- A Dipartimento di Scienze del Farmaco e della Salute, Università di Catania, Viale A. Doria 6, Catania, Italy.
| | - Maria Assunta Chiacchio
- A Dipartimento di Scienze del Farmaco e della Salute, Università di Catania, Viale A. Doria 6, Catania, Italy.
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6
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A computational study of TyrGly hydration. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.113011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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7
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Kumar A, Toal SE, DiGuiseppi D, Schweitzer-Stenner R, Wong BM. Water-Mediated Electronic Structure of Oligopeptides Probed by Their UV Circular Dichroism, Absorption Spectra, and Time-Dependent DFT Calculations. J Phys Chem B 2020; 124:2579-2590. [PMID: 32207305 DOI: 10.1021/acs.jpcb.0c00657] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigate the UV absorption spectra of a series of cationic GxG peptides (where x denotes a guest residue) in aqueous solution and find that only a subset of these spectra show a strong dependence with temperature. To explore whether or not this observation reflects conformational dependencies, we carry out time-dependent density functional calculations for the polyproline II (pPII) and β-strand conformations in implicit and explicit water. We find that the calculated CD spectra for pPII can qualitatively account for the experimental spectra irrespective of the water model. The β-strand UV-CD spectra, however, require the explicit consideration of water. Contrary to conventional wisdom, we find that both the NV1 and NV2 band are the envelopes of contributions from multiple transitions that involve more than just the HOMOs and LUMOs of the peptide groups. A natural transition orbital analysis reveals that some of the transitions have a charge-transfer character. The overall manifold of transitions depends on the peptide's backbone conformation, peptide hydration, and side chain of the guest residue. Our results reveal that peptide groups, side chains, and hydration shells must be considered as an entity for a physically valid characterization of UV absorbance and circular dichroism.
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Affiliation(s)
- Anshuman Kumar
- Department of Chemical & Environmental Engineering, Materials Science & Engineering Program, Department of Chemistry, and Department of Physics & Astronomy, University of California, Riverside, Riverside, California 92521, United States
| | - Siobhan E Toal
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - David DiGuiseppi
- Department of Chemistry, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | | | - Bryan M Wong
- Department of Chemical & Environmental Engineering, Materials Science & Engineering Program, Department of Chemistry, and Department of Physics & Astronomy, University of California, Riverside, Riverside, California 92521, United States
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8
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Lanza G, Chiacchio MA. Quantum Mechanics Study on Hydrophilic and Hydrophobic Interactions in the Trivaline-Water System. J Phys Chem B 2018; 122:4289-4298. [PMID: 29584432 DOI: 10.1021/acs.jpcb.8b00833] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the aim to elucidate hydrophobic effects in the unfolded state of peptides, DFT-M062X computations on the Val3H+· nH2O ( n up to 22) clusters have been accomplished. As far as the main chain is concerned, four conformers with β-strand and/or polyproline type II conformations, PPII (indicated as β-β, β-PPII, PPII-β, and PPII-PPII), have been found by changing the ϕ and ψ angles. For bare peptide, the side chain (isopropyl) of each residue can independently take on three different orientations with negligible effects on energetics. The great isopropyl spatial separations in β-β and β-PPII conformers allow for the construction of synergic and extensive water-water and water-peptide H-bonding in the minimal hydration Val3H+·22H2O models without significant steric encumbrance. Conversely, due to the proximity of the isopropyl of the central residue with the other two, some restrictions in the water shell construction around the peptide become evident for the PPII-PPII conformer and the number of energetically accessible structures decreases. This is indicative of correlated motion involving isopropyls and backbone mediated by water molecules, the origin of the nearest neighbor effects. Comparing the thermodynamic data of Ala3H+·22H2O and Val3H+·22H2O, what emerges is that both hydration enthalpy and entropy drive the β-strand stability of the latter.
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Affiliation(s)
- Giuseppe Lanza
- Dipartimento di Scienze del Farmaco , Università di Catania , Viale A. Doria 6 , Catania 95125 , Italy
| | - Maria A Chiacchio
- Dipartimento di Scienze del Farmaco , Università di Catania , Viale A. Doria 6 , Catania 95125 , Italy
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9
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Rubio-Martinez J, Tomas MS, Perez JJ. Effect of the solvent on the conformational behavior of the alanine dipeptide deduced from MD simulations. J Mol Graph Model 2017; 78:118-128. [PMID: 29055185 DOI: 10.1016/j.jmgm.2017.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/07/2017] [Accepted: 10/09/2017] [Indexed: 11/19/2022]
Abstract
In general, peptides do not exhibit a well-defined conformational profile in solution. However, despite the experimental blurred picture associated with their structure, compelling spectroscopic evidence shows that peptides exhibit local order. The conformational profile of a peptide is the result of a balance between intramolecular interactions between different atoms of the molecule and intermolecular interactions between atoms of the molecule and the solvent. Accordingly, the conformational profile of a peptide will change upon the properties of the solvent it is soaked. To get insight into the balance between intra- and intermolecular interactions on the conformational preferences of the peptide backbone we have studied the conformational profile of the alanine dipeptide in diverse solvents using molecular dynamics as sampling technique. Solvents studied include chloroform, methanol, dimethyl sulfoxide, water and N-methylacetamide. Different treatments of the solvent have been studied in the present work including explicit solvent molecules, a generalized Born model and using the bulk dielectric constant of the solvent. The diverse calculations identify four major conformations with different populations in the diverse solvents: the C7eq only sampled in chloroform; the C5 or extended conformation; the polyproline (PII) conformation and the right-handed α-helix conformation (αR). The results of present calculations permit to analyze how the balance between intra- and intermolecular interactions explains the populations of the diverse conformations observed.
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Affiliation(s)
- Jaime Rubio-Martinez
- Dept. of Physical Chemistry, Faculty of Chemistry, Universitat de Barcelona and the Institut de Recerca en Quimica Teorica i Computacional (IQTCUB), Mati i Franques 1-3, 08028 Barcelona, Spain
| | - M Santos Tomas
- Department of Architecture Technology, Universitat Politecnica de Catalunya, Av. Diagonal, 649, E-08028 Barcelona, Spain
| | - Juan J Perez
- Department of Chemical Engineering, Universitat Politecnica de Catalunya- Barcelona Tech, Av. Diagonal, 647, 08028 Barcelona, Spain.
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10
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Lanza G, Chiacchio MA. Quantum Mechanics Approach to Hydration Energies and Structures of Alanine and Dialanine. Chemphyschem 2017; 18:1586-1596. [PMID: 28371186 DOI: 10.1002/cphc.201700149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Indexed: 11/11/2022]
Abstract
A systematic approach to the phenomena related to hydration of biomolecules is reported at the state of the art of electronic-structure methods. Large-scale CCSD(T), MP4-SDQ, MP2, and DFT(M06-2X) calculations for some hydrated complexes of alanine and dialanine (Ala⋅13 H2 O, Ala2 H+ ⋅18 H2 O, and Ala2 ⋅18 H2 O) are compared with experimental data and other elaborate modeling to assess the reliability of a simple bottom-up approach. The inclusion of a minimal number of water molecules for microhydration of the polar groups together with the polarizable continuum model is sufficient to reproduce the relative bulk thermodynamic functions of the considered biomolecules. These quantities depend on the adopted electronic-structure method, which should be chosen with great care. Nevertheless, the computationally feasible MP2 and M06-2X functionals with the aug-cc-pVTZ basis set satisfactorily reproduce values derived by high-level CCSD(T) and MP4-SDQ methods, and thus they are suitable for future developments of more elaborate and hence more biochemically significant peptides.
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Affiliation(s)
- Giuseppe Lanza
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale A. Doria 6, Catania, 95125, Italy
| | - Maria A Chiacchio
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale A. Doria 6, Catania, 95125, Italy
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11
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DiGuiseppi D, Milorey B, Lewis G, Kubatova N, Farrell S, Schwalbe H, Schweitzer-Stenner R. Probing the Conformation-Dependent Preferential Binding of Ethanol to Cationic Glycylalanylglycine in Water/Ethanol by Vibrational and NMR Spectroscopy. J Phys Chem B 2017; 121:5744-5758. [DOI: 10.1021/acs.jpcb.7b02899] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | - Nina Kubatova
- Institut
für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität, 60438 Frankfurt am Main, Germany
| | | | - Harald Schwalbe
- Institut
für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität, 60438 Frankfurt am Main, Germany
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12
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Lanza G, Chiacchio MA. Effects of Hydration on the Zwitterion Trialanine Conformation by Electronic Structure Theory. J Phys Chem B 2016; 120:11705-11719. [DOI: 10.1021/acs.jpcb.6b08108] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Giuseppe Lanza
- Dipartimento
di Scienze del
Farmaco, Università di Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Maria A. Chiacchio
- Dipartimento
di Scienze del
Farmaco, Università di Catania, Viale A. Doria 6, 95125 Catania, Italy
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13
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Conformational analysis of short polar side-chain amino-acids through umbrella sampling and DFT calculations. J Mol Model 2016; 22:273. [PMID: 27783230 DOI: 10.1007/s00894-016-3139-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 10/09/2016] [Indexed: 10/20/2022]
Abstract
Molecular and quantum mechanics calculations were carried out in a series of tripeptides (GXG, where X = D, N and C) as models of the unfolded states of proteins. The selected central amino acids, especially aspartic acid (D) and asparagine (N) are known to present significant average conformations in partially allowed areas of the Ramachandran plot, which have been suggested to be important in unfolded protein regions. In this report, we present the calculation of the propensity values through an umbrella sampling procedure in combination with the calculation of the NMR J-coupling constants obtained by a DFT model. The experimental NMR observations can be reasonably explained in terms of a conformational distribution where PPII and β basins sum up propensities above 0.9. The conformational analysis of the side chain dihedral angle (χ1), along with the computation of 3J(HαHβ), revealed a preference for the g - and g + rotamers. These may be connected with the presence of intermolecular H-bonding and carbonyl-carbonyl interactions sampled in the PPII and β basins. Taking into account all those results, it can be established that these residues show a similar behavior to other amino acids in short peptides regarding backbone φ,ψ dihedral angle distribution, in agreement with some experimental analysis of capped dipeptides.
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14
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Ilawe NV, Raeber AE, Schweitzer-Stenner R, Toal SE, Wong BM. Assessing backbone solvation effects in the conformational propensities of amino acid residues in unfolded peptides. Phys Chem Chem Phys 2016; 17:24917-24. [PMID: 26343224 DOI: 10.1039/c5cp03646a] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Conformational ensembles of individual amino acid residues within model GxG peptides (x representing different amino acid residues) are dominated by a mixture of polyproline II (pPII) and β-strand like conformations. We recently discovered rather substantial differences between the enthalpic and entropic contributions to this equilibrium for different amino acid residues. Isoleucine and valine exceed all other amino acid residues in terms of their rather large enthalpic stabilization and entropic destabilization of polyproline II. In order to shed light on these underlying physical mechanisms, we performed high-level DFT calculations to explore the energetics of four representative GxG peptides where x = alanine (A), leucine (L), valine (V), and isoleucine (I) in explicit water (10 H2O molecules with a polarizable continuum water model) and in vacuo. We found that the large energetic contributions to the stabilization of pPII result, to a major extent, from peptide-water, water-water interactions, and changes of the solvent self-energy. Differences between the peptide-solvent interaction energies of hydration in pPII and β-strand peptides are particularly important for the pPII ⇌ β equilibria of the more aliphatic peptides GIG and GLG. Furthermore, we performed a vibrational analysis of the four peptides in both conformations and discovered a rather substantial mixing between water motions and peptide vibrations below 700 cm(-1). We found that the respective vibrational entropies are substantially different for the considered conformations, and their contributions to the Gibbs/Helmholtz energy stabilize β-strand conformations. Taken together, our results underscore the notion of the solvent being the predominant determinant of peptide (and protein) conformations in the unfolded state.
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Affiliation(s)
- Niranjan V Ilawe
- Department of Chemical & Environmental Engineering, and Materials Science & Engineering Program, University of California, Riverside, 900 University Avenue, Riverside, CA 92521, USA.
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15
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Almeida GG, Cordeiro JMM, Martín ME, Aguilar MA. Conformational Changes of the Alanine Dipeptide in Water–Ethanol Binary Mixtures. J Chem Theory Comput 2016; 12:1514-24. [DOI: 10.1021/acs.jctc.5b00952] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Glauco G. Almeida
- Faculdade de Engenharia,
Universidade Estadual Paulista “Julio de Mesquita Filho″, Ilha Solteira 15385-000, Brasil
| | - João M. M. Cordeiro
- Faculdade de Engenharia,
Universidade Estadual Paulista “Julio de Mesquita Filho″, Ilha Solteira 15385-000, Brasil
| | - M. Elena Martín
- Área
de Química Física, University of Extremadura, Avda.
Elvas s/n, Edif. José Ma Viguera
Lobo, 3a planta, Badajoz 06006, Spain
| | - Manuel A. Aguilar
- Área
de Química Física, University of Extremadura, Avda.
Elvas s/n, Edif. José Ma Viguera
Lobo, 3a planta, Badajoz 06006, Spain
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16
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Meral D, Toal S, Schweitzer-Stenner R, Urbanc B. Water-Centered Interpretation of Intrinsic pPII Propensities of Amino Acid Residues: In Vitro-Driven Molecular Dynamics Study. J Phys Chem B 2015; 119:13237-51. [PMID: 26418575 DOI: 10.1021/acs.jpcb.5b06281] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amino acid residues of unfolded peptides in water sample only a few basins in the Ramachandran plot, including prominent polyproline II-like (pPII) conformations. Dynamics of guest residues, X, in GXG peptides in water were recently reported to be dominated by pPII and β-strand-like (β) conformations, resulting in an enthalpy-entropy compensation at ∼300 K. Using molecular dynamics (MD) in explicit solvent, we here examine pPII and β conformational ensembles of 15 guest residues in GXG peptides, quantify local orientation of water around their side chains through novel water orientation plots, and study their hydration and hydrogen bonding properties. We show that pPII and β ensembles are characterized by distinct water orientations: pPII ensembles are associated with an increased population of water oriented in parallel to the side chain surface whereas β ensembles exhibit more heterogeneous water orientations. The backbone hydration is significantly higher in pPII than in β ensembles. Importantly, pPII to β hydration differences and the solvent accessible surface area of Cβ hydrogens both correlate with experimental pPII propensities. We propose that pPII conformations are stabilized by a local, hydrogen-bonded clathrate-like water structure and that residue-specific intrinsic pPII propensities reflect distinct abilities of side chains to template this water structure.
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Affiliation(s)
- Derya Meral
- Department of Physics, Drexel University , Philadelphia, Pennsylvania 19104, United States
| | - Siobhan Toal
- Department of Chemistry, Drexel University , Philadelphia, Pennsylvania 19104, United States
| | | | - Brigita Urbanc
- Department of Physics, Drexel University , Philadelphia, Pennsylvania 19104, United States.,Faculty of Mathematics and Physics, University of Ljubljana , 1000 Ljubljana, Slovenia
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17
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Lanza G, Chiacchio MA. Interfacial water at the trialanine hydrophilic surface: a DFT electronic structure and bottom-up investigation. Phys Chem Chem Phys 2015; 17:17101-11. [DOI: 10.1039/c5cp00270b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A model describing a network of hydrogen bonded water-trialanine has been developed to estimate hydration effects on various conformers of the peptide.
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Affiliation(s)
- Giuseppe Lanza
- Dipartimento di Scienze del Farmaco
- Università di Catania
- 95125 Catania
- Italy
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