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Sheng M, Silvestrini F, Biczysko M, Puzzarini C. Structural and Vibrational Properties of Amino Acids from Composite Schemes and Double-Hybrid DFT: Hydrogen Bonding in Serine as a Test Case. J Phys Chem A 2021; 125:9099-9114. [PMID: 34623165 DOI: 10.1021/acs.jpca.1c06993] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The structures, relative stabilities, and vibrational wavenumbers of the two most stable conformers of serine, stabilized by the O-H···N, O-H···O═C and N-H···O-H intramolecular hydrogen bonds, have been evaluated by means of state-of-the-art composite schemes based on coupled-cluster (CC) theory. The so-called "cheap" composite approach (CCSD(T)/(CBS+CV)MP2) allowed determination of accurate equilibrium structures and harmonic vibrational wavenumbers, also pointing out significant corrections beyond the CCSD(T)/cc-pVTZ level. These accurate results stand as a reference for benchmarking selected hybrid and double-hybrid, dispersion-corrected DFT functionals. B2PLYP-D3 and DSDPBEP86 in conjunction with a triple-ζ basis set have been confirmed as effective methodologies for structural and spectroscopic studies of medium-sized flexible biomolecules, also showing intramolecular hydrogen bonding. These best performing double-hybrid functionals have been employed to simulate IR spectra by means of vibrational perturbation theory, also considering hybrid CC/DFT schemes. The best overall agreement with experiment, with mean absolute error of 8 cm-1, has been obtained by combining CCSD(T)/(CBS+CV)MP2 harmonic wavenumbers with B2PLYP-D3/maug-cc-pVTZ anharmonic corrections. Finally, a composite scheme entirely based on CCSD(T) calculations (CCSD(T)/CBS+CV) has been employed for energetics, further confirming that serine II is the most stable conformer, also when zero-point vibrational energy corrections are included.
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Affiliation(s)
- Mingzhu Sheng
- International Centre for Quantum and Molecular Structures, Physics Department, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Filippo Silvestrini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Malgorzata Biczysko
- International Centre for Quantum and Molecular Structures, Physics Department, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Cristina Puzzarini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, 40126 Bologna, Italy
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2
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Zhu S, Kachooei E, Harmer JR, Brown LJ, Separovic F, Sani MA. TOAC spin-labeled peptides tailored for DNP-NMR studies in lipid membrane environments. Biophys J 2021; 120:4501-4511. [PMID: 34480924 DOI: 10.1016/j.bpj.2021.08.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 07/08/2021] [Accepted: 08/10/2021] [Indexed: 12/15/2022] Open
Abstract
The benefit of combining in-cell solid-state dynamic nuclear polarization (DNP) NMR and cryogenic temperatures is providing sufficient signal/noise and preservation of bacterial integrity via cryoprotection to enable in situ biophysical studies of antimicrobial peptides. The radical source required for DNP was delivered into cells by adding a nitroxide-tagged peptide based on the antimicrobial peptide maculatin 1.1 (Mac1). In this study, the structure, localization, and signal enhancement properties of a single (T-MacW) and double (T-T-MacW) TOAC (2,2,6,6-tetramethylpiperidine-N-oxyl-4-amino-4-carboxylic acid) spin-labeled Mac1 analogs were determined within micelles or lipid vesicles. The solution NMR and circular dichroism results showed that the spin-labeled peptides adopted helical structures in contact with micelles. The peptides behaved as an isolated radical source in the presence of multilamellar vesicles, and the electron paramagnetic resonance (EPR) electron-electron distance for the doubly spin-labeled peptide was ∼1 nm. The strongest paramagnetic relaxation enhancement (PRE) was observed for the lipid NMR signals near the glycerol-carbonyl backbone and was stronger for the doubly spin-labeled peptide. Molecular dynamics simulation of the T-T-MacW radical source in phospholipid bilayers supported the EPR and PRE observations while providing further structural insights. Overall, the T-T-MacW peptide achieved better 13C and 15N signal NMR enhancements and 1H spin-lattice T1 relaxation than T-MacW.
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Affiliation(s)
- Shiying Zhu
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Ehsan Kachooei
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Jeffrey R Harmer
- Centre for Advanced Imaging, University of Queensland, Brisbane, Queensland, Australia
| | - Louise J Brown
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Frances Separovic
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Marc-Antoine Sani
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.
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3
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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
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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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4
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Guo C, Yu J, Horsley JR, Sheves M, Cahen D, Abell AD. Backbone-Constrained Peptides: Temperature and Secondary Structure Affect Solid-State Electron Transport. J Phys Chem B 2019; 123:10951-10958. [PMID: 31777245 DOI: 10.1021/acs.jpcb.9b07753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The primary sequence and secondary structure of a peptide are crucial to charge migration, not only in solution (electron transfer, ET), but also in the solid-state (electron transport, ETp). Hence, understanding the charge migration mechanisms is fundamental to the development of biomolecular devices and sensors. We report studies on four Aib-containing helical peptide analogues: two acyclic linear peptides with one and two electron-rich alkene-based side chains, respectively, and two peptides that are further rigidified into a macrocycle by a side bridge constraint, containing one or no alkene. ETp was investigated across Au/peptide/Au junctions, between 80 and 340 K in combination with the molecular dynamic (MD) simulations. The results reveal that the helical structure of the peptide and electron-rich side chain both facilitate the ETp. As temperature increases, the loss of helical structure, change of monolayer tilt angle, and increase of thermally activated fluctuations affect the conductance of peptides. Specifically, room temperature conductance across the peptide monolayers correlates well with previously observed ET rate constants, where an interplay between backbone rigidity and electron-rich side chains was revealed. Our findings provide new means to manipulate electronic transport across solid-state peptide junctions.
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Affiliation(s)
- Cunlan Guo
- Department of Materials and Interfaces , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Jingxian Yu
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Institute of Photonics and Advanced Sensing (IPAS), Department of Chemistry , The University of Adelaide , Adelaide , South Australia 5005 , Australia
| | - John R Horsley
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Institute of Photonics and Advanced Sensing (IPAS), Department of Chemistry , The University of Adelaide , Adelaide , South Australia 5005 , Australia
| | - Mordechai Sheves
- Department of Materials and Interfaces , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - David Cahen
- Department of Materials and Interfaces , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Andrew D Abell
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Institute of Photonics and Advanced Sensing (IPAS), Department of Chemistry , The University of Adelaide , Adelaide , South Australia 5005 , Australia
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5
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Elenewski JE, Velizhanin KA, Zwolak M. A spin-1 representation for dual-funnel energy landscapes. J Chem Phys 2018; 149:035101. [PMID: 30037251 PMCID: PMC7723752 DOI: 10.1063/1.5036677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The interconversion between the left- and right-handed helical folds of a polypeptide defines a dual-funneled free energy landscape. In this context, the funnel minima are connected through a continuum of unfolded conformations, evocative of the classical helix-coil transition. Physical intuition and recent conjectures suggest that this landscape can be mapped by assigning a left- or right-handed helical state to each residue. We explore this possibility using all-atom replica exchange molecular dynamics and an Ising-like model, demonstrating that the energy landscape architecture is at odds with a two-state picture. A three-state model-left, right, and unstructured-can account for most key intermediates during chiral interconversion. Competing folds and excited conformational states still impose limitations on the scope of this approach. However, the improvement is stark: Moving from a two-state to a three-state model decreases the fit error from 1.6 kBT to 0.3 kBT along the left-to-right interconversion pathway.
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Affiliation(s)
- Justin E. Elenewski
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
- Maryland Nanocenter, University of Maryland, College Park, MD 20742, USA
| | | | - Michael Zwolak
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
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Chandramouli B, Del Galdo S, Mancini G, Tasinato N, Barone V. Tailor-made computational protocols for precise characterization of small biological building blocks using QM and MM approaches. Biopolymers 2018. [DOI: 10.1002/bip.23109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Balasubramanian Chandramouli
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
- Compunet, Istituto Italiano di Tecnologia, via Morego 30; Genova Italy
| | - Sara Del Galdo
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
| | - Giordano Mancini
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3; Pisa 56127 Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3; Pisa 56127 Italy
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Grubišić S, Chandramouli B, Barone V, Brancato G. Chain length, temperature and solvent effects on the structural properties of α-aminoisobutyric acid homooligopeptides. Phys Chem Chem Phys 2018; 18:20389-98. [PMID: 27402118 DOI: 10.1039/c6cp01120a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Non-coded α-amino acids, originally exploited by nature, have been successfully reproduced by recent synthetic strategies to confer special structural and functional properties to small peptides. The most known and well-studied atypical residue is α-aminoisobutyric acid (Aib), which is contained in a fairly large number of peptides with known antibiotic effects. Here, we report on a molecular dynamics (MD) study of a series of homooligopeptides based on α-aminoisobutyric acid (Aib) with increasing length (Ac-(Aib)n-NMe, n = 5, 6, 7 and 10) and at various temperatures, employing a recent extension of the AMBER force field tailored for the Aib residue. Solvent effects have been analyzed by comparative MD simulations of a heptapeptide in water and dimethylsulfoxide at different temperatures. Our results show that the preference for the 310- and/or α-helix structures, which typically characterize Aib based peptides, is finely tuned by several factors including the chain length, temperature and solvent nature. While the transitions between intra-molecular i → i + 3 and i → i + 4 hydrogen bonds characterizing 310 and α-helices, respectively, are rather fast in small peptides (in the picosecond timescale), our analysis shows that the above physical and chemical factors modulate the relative equilibrium populations of the two helical structures. The obtained results nicely agree with available experimental data and support the use of the new force field for modeling Aib containing peptides.
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Affiliation(s)
- Sonja Grubišić
- Center for Chemistry, IHTM, University of Belgrade, Njegoševa 12, P.O. Box 815, 11001 Belgrade, Serbia.
| | - Balasubramanian Chandramouli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy. and Istituto Nazionale di Fisica Nucleare, Largo Pontecorvo 3, I-56100 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy. and Istituto Nazionale di Fisica Nucleare, Largo Pontecorvo 3, I-56100 Pisa, Italy
| | - Giuseppe Brancato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy. and Istituto Nazionale di Fisica Nucleare, Largo Pontecorvo 3, I-56100 Pisa, Italy
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8
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Jiang Z, Biczysko M, Moriarty NW. Accurate geometries for “Mountain pass” regions of the Ramachandran plot using quantum chemical calculations. Proteins 2018; 86:273-278. [DOI: 10.1002/prot.25451] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 12/16/2017] [Accepted: 01/01/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Zhongming Jiang
- International Centre for Quantum and Molecular Structures, College of Sciences; Shanghai University, 99 Shangda Road; 200444 Shanghai China
| | - Malgorzata Biczysko
- International Centre for Quantum and Molecular Structures, College of Sciences; Shanghai University, 99 Shangda Road; 200444 Shanghai China
| | - Nigel W. Moriarty
- Molecular Biophysics and Integrated Bioimaging Division; Lawrence Berkeley National Laboratory; Berkeley California 94720
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9
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Wałęsa R, Broda MA. The influence of solvent on conformational properties of peptides with Aib residue-a DFT study. J Mol Model 2017; 23:349. [PMID: 29164349 PMCID: PMC5698364 DOI: 10.1007/s00894-017-3508-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/24/2017] [Indexed: 12/30/2022]
Abstract
The conformational propensities of the Aib residue on the example of two model peptides Ac-Aib-NHMe (1) and Ac-Aib-NMe2 (2), were studied by B3LYP and M06-2X functionals, in the gas phase and in the polar solvents. To verify the reliability of selected functionals, we also performed MP2 calculations for the tested molecules in vacuum. Polarizable continuum models (PCM and SMD) were used to estimate the solvent effect. Ramachandran maps were calculated to find all energy minima. Noncovalent intramolecular interactions due to hydrogen-bonds and dipole attractions between carbonyl groups are responsible for the relative stabilities of the conformers. In order to verify the theoretical results, the available conformations of similar X-ray structures from the Cambridge Crystallographic Data Center (CCDC) were analyzed. The results of the calculations show that both derivatives with the Aib residue in the gas phase prefer structures stabilized by intramolecular N-H⋯O hydrogen bonds, i.e., C5 and C7 conformations, while polar solvent promotes helical conformation with φ, ψ values equal to +/-60°, +/-40°. In addition, in the case of molecule 2, the helical conformation is the only one available in the polar environment. This result is fully consistent with the X-ray data. Graphical abstract Effect of solvent on the Ramachandran maps of the model peptides with Aib residue.
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Affiliation(s)
- Roksana Wałęsa
- Faculty of Chemistry, University of Opole, 48, Oleska St., 45-052 Opole, Poland
| | - Małgorzata A. Broda
- Faculty of Chemistry, University of Opole, 48, Oleska St., 45-052 Opole, Poland
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10
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Bocchinfuso G, Conflitti P, Raniolo S, Caruso M, Mazzuca C, Gatto E, Placidi E, Formaggio F, Toniolo C, Venanzi M, Palleschi A. Aggregation propensity of Aib homo-peptides of different length: an insight from molecular dynamics simulations. J Pept Sci 2014; 20:494-507. [DOI: 10.1002/psc.2648] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 04/16/2014] [Accepted: 04/16/2014] [Indexed: 12/18/2022]
Affiliation(s)
- Gianfranco Bocchinfuso
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Paolo Conflitti
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Stefano Raniolo
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Mario Caruso
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Claudia Mazzuca
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Emanuela Gatto
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Ernesto Placidi
- Department of Physics; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
- CNR-ISM; Via Fosso del Cavaliere 100 I-00133 Roma Italy
| | - Fernando Formaggio
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry; University of Padova; I-35131 Padua Italy
| | - Claudio Toniolo
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry; University of Padova; I-35131 Padua Italy
| | - Mariano Venanzi
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Antonio Palleschi
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
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11
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A new AMBER-compatible force field parameter set for alkanes. J Mol Model 2014; 20:2143. [DOI: 10.1007/s00894-014-2143-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 01/10/2014] [Indexed: 10/25/2022]
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