Ramachandran Plot for Alanine Dipeptide as Determined from Raman Optical Activity

Parchaňský, Václav; Kapitán, Josef; Kaminský, Jakub; Šebestı́k, Jaroslav; Bouř, Petr

doi:10.1021/jz401366j

Cited by 56 publications

(63 citation statements)

References 55 publications

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“…(d) in Ref. which we have reproduced as Fig. ] is much more consistent with the experimental plots for alanine residues [Fig.…”

Section: Discussionsupporting

confidence: 87%

“…In contrast to the above discussed quantum mechanical Ramachandran plots, the one reported by Parchansky et al . using the mPWPLYPD/6–311++G**/SMD theory [Fig.…”

Section: Discussionmentioning

confidence: 90%

“…We have compared the empirical protein energy maps (EPEMs) with a few of the recently published ( ϕ , ψ ) plots obtained from theoretical models . Specifically, we have used the plots published in references for such comparative analyses. In addition, we have compared the experimental plots with an energy map of alanine dipeptide obtained by employing OPLS‐2005 force field [Jubilant Biosys, personal communications] in the Schrodinger software Maestro.…”

Section: Discussionmentioning

confidence: 99%

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Experimental conformational energy maps of proteins and peptides

et al. 2017

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We have presented an extensive analysis of the peptide backbone dihedral angles in the PDB structures and computed experimental Ramachandran plots for their distributions seen under a various constraints on X-ray resolution, representativeness at different sequence identity percentages, and hydrogen bonding distances. These experimental distributions have been converted into isoenergy contour plots using the approach employed previously by F. M. Pohl. This has led to the identification of energetically favored minima in the Ramachandran (ϕ, ψ) plots in which global minima are predominantly observed either in the right-handed α-helical or the polyproline II regions. Further, we have identified low energy pathways for transitions between various minima in the (ϕ,ψ) plots. We have compared and presented the experimental plots with published theoretical plots obtained from both molecular mechanics and quantum mechanical approaches. In addition, we have developed and employed a root mean square deviation (RMSD) metric for isoenergy contours in various ranges, as a measure (in kcal.mol ) to compare any two plots and determine the extent of correlation and similarity between their isoenergy contours. In general, we observe a greater degree of compatibility with experimental plots for energy maps obtained from molecular mechanics methods compared to most quantum mechanical methods. The experimental energy plots we have investigated could be helpful in refining protein structures obtained from X-ray, NMR, and electron microscopy and in refining force field parameters to enable simulations of peptide and protein structures that have higher degree of consistency with experiments. Proteins 2017; 85:979-1001. © 2017 Wiley Periodicals, Inc.

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“…(d) in Ref. which we have reproduced as Fig. ] is much more consistent with the experimental plots for alanine residues [Fig.…”

Section: Discussionsupporting

confidence: 87%

“…In contrast to the above discussed quantum mechanical Ramachandran plots, the one reported by Parchansky et al . using the mPWPLYPD/6–311++G**/SMD theory [Fig.…”

Section: Discussionmentioning

confidence: 90%

Section: Discussionmentioning

confidence: 99%

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Experimental conformational energy maps of proteins and peptides

et al. 2017

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“…2,7 Especially the chiroptical variant of Raman spectroscopy, Raman optical activity (ROA), is very sensitive to the three-dimensional solution structure and dynamics of biomolecules. 8,9 It has been applied to study the solution structure of peptides [10][11][12] , proteins [13][14][15] , glycoproteins [16][17][18] , complex sugars 19 and even intact viruses [20][21][22] . While the unique conformational sensitivity of ROA is recognised, the biggest challenge lies in the detailed interpretation of the experimental ROA patterns.…”

Section: Introductionmentioning

confidence: 99%

Ramachandran mapping of peptide conformation using a large database of computed Raman and Raman optical activity spectra

Mensch

Barron

Johannessen

2016

Phys. Chem. Chem. Phys.

136

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The past decades, Raman optical activity (ROA) spectroscopy has been shown to be very sensitive to the solution structure of peptides and proteins. A major and urgent challenge remains the need to make detailed assignments of experimental ROA patterns and relate those to the solution structure adopted by the protein. The past years, theoretical developments and implementations of ROA theory have made it possible to use quantum chemical methods to compute ROA spectra of peptides. In this work, a large database of ROA spectra of peptide model structures describing the allowed backbone conformations of proteins were systematically calculated and used to make unprecedented detailed assignments of experimental ROA patterns to the conformational elements of the peptide in solution. By using a similarity index to compare an experimental spectrum to the database spectra (2902 theoretical spectra), the conformational preference of the peptide in solution can be assigned to a very specific region in the Ramachandran space. For six (poly)peptides this approach was validated and gives excellent agreement between experiment and theory. Additionally, hydrogen/deuterium exchanged structures and the conformational dependence of the amide modes in Raman spectra can be analysed using the new database. The excellent agreement between experiment and theory demonstrates the power of the newly developed database as a tool to study Raman and ROA patterns of peptides and proteins. The interpretation of experimental ROA patterns of different proteins published in scientific literature is discussed based on the spectral trends observed in the database.

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“…However, determining the conformational sampling of these short peptides is challenging because ensembles of structures rapidly interconvert in solution. 19–20, 23–24 Multiple spectroscopic techniques have been used to investigate this problem, from the simplest systems of trialanine 10–12, 16–19, 25–26 and Ac-Ala-NHMe (Ac: acetyl) 27–29 with only two peptide bonds, to longer alanine-rich peptides including (Ala) n (n = 4 – 7) 6, 13–14, 20 and Ac-X 2 A 7 O 2 -NH 2 (XAO, here X = diaminobutyric acid, and O = ornithine), 5, 15, 21–22 and host–guest peptides like GGXGG. 7–8 Kim et al suggested ppII-like conformation for Ac-Ala-NHMe in aqueous solution, employing 2D IR in combination with DFT calculation.…”

Section: Introductionmentioning

confidence: 99%

Structure of Penta-Alanine Investigated by Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation

et al. 2016

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We have studied the structure of (Ala)5, a model unfolded peptide, using a combination of 2D IR spectroscopy and molecular dynamics (MD) simulation. Two different isotopomers, each bis-labeled with 13C=O and 13C=18O, were strategically designed to shift individual site frequencies and uncouple neighboring amide-I′ modes. 2D IR spectra taken under the double-crossed 〈π/4, −π/4, Y, Z〉 polarization show that the labeled four-oscillator systems can be approximated by three two-oscillator systems. By utilizing the different polarization dependence of diagonal and cross peaks, we extracted the coupling constants and angles between three pairs of amide-I transition dipoles through spectral fitting. These parameters were related to the peptide backbone dihedral angles through DFT calculated maps. The derived dihedral angles are all located in the polyproline-II (ppII) region of the Ramachandran plot. These results were compared to the conformations sampled by Hamiltonian replica-exchange MD simulations with three different CHARMM force fields. The C36 force field predicted that ppII is the dominant conformation, consistent with the experimental findings, whereas C22/CMAP predicted similar population for α+, β, and ppII, and the polarizable Drude-2013 predicted dominating β structure. Spectral simulation based on MD representative conformations and structure ensembles demonstrated the need to include multiple 2D spectral features, especially the cross-peak intensity ratio and shape, in structure determination. Using 2D reference spectra defined by the C36 structure ensemble, the best spectral simulation is achieved with nearly 100% ppII population, although the agreement with the experimental cross-peak intensity ratio is still insufficient. The dependence of population determination on the choice of reference structures/spectra and the current limitations on theoretical modeling relating peptide structures to spectral parameters are discussed. Compared with the previous results on alanine based oligopeptides, the dihedral angles of our fitted structure and the most populated ppII structure from the C36 simulation are in good agreement with those suggesting a major ppII population. Our results provide further support for the importance of ppII conformation in the ensemble of unfolded peptides.

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Ramachandran Plot for Alanine Dipeptide as Determined from Raman Optical Activity

Cited by 56 publications

References 55 publications

Experimental conformational energy maps of proteins and peptides

Experimental conformational energy maps of proteins and peptides

Ramachandran mapping of peptide conformation using a large database of computed Raman and Raman optical activity spectra

Structure of Penta-Alanine Investigated by Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation

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