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Samantha Jenkins - One of the best experts on this subject based on the ideXlab platform.
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the role of weak interactions in characterizing peptide folding preferences using a qtaim interpretation of the Ramachandran Plot ϕ ψ
International Journal of Quantum Chemistry, 2018Co-Authors: Roya Momen, Sergei Manzhos, Alireza Azizi, Steven R Kirk, Lingling Wang, Ping Yang, Samantha JenkinsAbstract:The original Ramachandran Plot is a potent way to understand structures of biomolecules, however only backbone conformations are considered. We formulate a new interpretation of the original Ramachandran Plot (ϕ-ψ) that can include a description of the weaker interactions including both the hydrogen bonds and HH bonds as a new way to derive insights into the phenomenon of peptide folding. Specifically, we show that QTAIM analysis permits identifying key regions of the Ramachandran Plot without the need for massive data sets. The QTAIM interpreted Ramachandran Plot is derived from QTAIM eigenvectors and not a trivial coordinate transformation. An investigation of both the backbone and the weaker bonds within the framework of the QTAIM interpreted Ramachandran Plot was found to be in line with physical intuition. The least-preferred directions calculated for the hydrogen bonds and HH bonds were found to coincide with the “unlikely” regions of the Ramachandran Plot.
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Exploration of the forbidden regions of the Ramachandran Plot (ϕ-ψ) with QTAIM
Physical Chemistry Chemical Physics, 2017Co-Authors: Roya Momen, Tianlv Xu, Wenxuan Li, Sergei Manzhos, Alireza Azizi, Steven R Kirk, Lingling Wang, Yang Ping, Samantha JenkinsAbstract:A new QTAIM interpretation of the Ramachandran Plot is formulated from the most and least facile eigenvectors of the second-derivative matrix of the electron density with a set of 29 magainin-2 peptide conformers. The presence of QTAIM eigenvectors associated with the most and least preferred directions of electronic charge density explained the role of hydrogen bonding, H⋯H contacts and the glycine amino acid monomer in peptide folding. The highest degree of occupation of the QTAIM interpreted Ramachandran Plot was found for the glycine amino acid monomer compared with the remaining backbone peptide bonds. The mobility of the QTAIM eigenvectors of the glycine amino acid monomer was higher than for the other amino acids and was comparable to that of the hydrogen bonding, explaining the flexibility of the magainin-2 backbone. We experimented with a variety of hybrid QTAIM–Ramachandran Plots to highlight and explain why the glycine amino acid monomer largely occupies the ‘forbidden’ region on the Ramachandran Plot. In addition, the new hybrid QTAIM–Ramachandran Plots contained recognizable regions that can be associated with concepts familiar from the conventional Ramachandran Plot whilst retaining the character of the QTAIM most and least preferred regions.
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The Role of Weak Interactions in Characterizing Peptide Folding Preferences using a QTAIM Interpretation of the Ramachandran Plot ({\phi}-{\psi})
International Journal of Quantum Chemistry, 2017Co-Authors: Roya Momen, Sergei Manzhos, Alireza Azizi, Steven R Kirk, Lingling Wang, Yang Ping, Samantha JenkinsAbstract:The Ramachandran Plot is a potent way to understand structures of biomolecules, however, the original formulation of the Ramachandran Plot only considers backbone conformations. We formulate a new interpretation of the original Ramachandran Plot ($\phi-\psi$) that can include a description of the weaker interactions including both the hydrogen bonds and H$---$H bonds as a new way to derive insights into the phenomenon of peptide folding. We use QTAIM (quantum theory of atoms in molecules) to interpret the Ramachandran Plot. Specifically, we show that QTAIM analysis permits identifying key regions of the Ramachandran Plot without the need for massive data sets. A highly non-linear relationship is found between the QTAIM vector-derived interpreted Ramachandran Plot and the conventional Ramachandran Plot ($\phi-\psi$) demonstrating that this new approach is not a trivial coordinate transformation. An investigation of both the backbone and the weaker bonds within the framework of the QTAIM interpreted Ramachandran Plot was found to be in line with physical intuition. The least-preferred directions calculated for the hydrogen bonds and H$---$H bonds were found to coincide with the 'unlikely' regions of the Ramachandran Plot.
Robert Brasseur - One of the best experts on this subject based on the ideXlab platform.
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Revisiting the Ramachandran Plot: Hard‐sphere repulsion, electrostatics, and H‐bonding in the α‐helix
Protein science : a publication of the Protein Society, 2009Co-Authors: Annick Thomas, Robert BrasseurAbstract:What determines the shape of the allowed regions in the Ramachandran Plot? Although Ramachandran explained these regions in terms of 1–4 hard-sphere repulsions, there are discrepancies with the data where, in particular, the αR, αL, and β-strand regions are diagonal. The αR-region also varies along the α-helix where it is constrained at the center and the amino terminus but diffuse at the carboxyl terminus. By analyzing a high-resolution database of protein structures, we find that certain 1–4 hard-sphere repulsions in the standard steric map of Ramachandran do not affect the statistical distributions. By ignoring these steric clashes (N···Hi+1 and Oi−1···C), we identify a revised set of steric clashes (Cβ···O, Oi−1···Ni+1, Cβ···Ni+1, Oi−1···Cβ, and Oi−1···O) that produce a better match with the data. We also find that the strictly forbidden region in the Ramachandran Plot is excluded by multiple steric clashes, whereas the outlier region is excluded by only one significant steric clash. However, steric clashes alone do not account for the diagonal regions. Using electrostatics to analyze the conformational dependence of specific interatomic interactions, we find that the diagonal shape of the αR and αL-regions also depends on the optimization of the N···Hi+1 and Oi−1···C interactions, and the diagonal β-strand region is due to the alignment of the CO and NH dipoles. Finally, we reproduce the variation of the Ramachandran Plot along the α-helix in a simple model that uses only H-bonding constraints. This allows us to rationalize the difference between the amino terminus and the carboxyl terminus of the α-helix in terms of backbone entropy.
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revisiting the Ramachandran Plot hard sphere repulsion electrostatics and h bonding in the α helix
Protein Science, 2009Co-Authors: Annick Thomas, Robert BrasseurAbstract:What determines the shape of the allowed regions in the Ramachandran Plot? Although Ramachandran explained these regions in terms of 1–4 hard-sphere repulsions, there are discrepancies with the data where, in particular, the αR, αL, and β-strand regions are diagonal. The αR-region also varies along the α-helix where it is constrained at the center and the amino terminus but diffuse at the carboxyl terminus. By analyzing a high-resolution database of protein structures, we find that certain 1–4 hard-sphere repulsions in the standard steric map of Ramachandran do not affect the statistical distributions. By ignoring these steric clashes (N···Hi+1 and Oi−1···C), we identify a revised set of steric clashes (Cβ···O, Oi−1···Ni+1, Cβ···Ni+1, Oi−1···Cβ, and Oi−1···O) that produce a better match with the data. We also find that the strictly forbidden region in the Ramachandran Plot is excluded by multiple steric clashes, whereas the outlier region is excluded by only one significant steric clash. However, steric clashes alone do not account for the diagonal regions. Using electrostatics to analyze the conformational dependence of specific interatomic interactions, we find that the diagonal shape of the αR and αL-regions also depends on the optimization of the N···Hi+1 and Oi−1···C interactions, and the diagonal β-strand region is due to the alignment of the CO and NH dipoles. Finally, we reproduce the variation of the Ramachandran Plot along the α-helix in a simple model that uses only H-bonding constraints. This allows us to rationalize the difference between the amino terminus and the carboxyl terminus of the α-helix in terms of backbone entropy.
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The Ramachandran Plots of glycine and pre-proline
BMC structural biology, 2005Co-Authors: Robert BrasseurAbstract:The Ramachandran Plot is a fundamental tool in the analysis of protein structures. Of the 4 basic types of Ramachandran Plots, the interactions that determine the generic and proline Ramachandran Plots are well understood. The interactions of the glycine and pre-proline Ramachandran Plots are not. In glycine, the ψ angle is typically clustered at ψ = 180° and ψ = 0°. We show that these clusters correspond to conformations where either the Ni+1 or O atom is sandwiched between the two Hα atoms of glycine. We show that the shape of the 5 distinct regions of density (the α, αL, βS, βP and βPR regions) can be reproduced with electrostatic dipole-dipole interactions. In pre-proline, we analyse the origin of the ζ region of the Ramachandran Plot, a region unique to pre-proline. We show that it is stabilized by a COi-1···CδHδi+1 weak hydrogen bond. This is analogous to the COi-1···NHi+1 hydrogen bond that stabilizes the γ region in the generic Ramachandran Plot. We have identified the specific interactions that affect the backbone of glycine and pre-proline. Knowledge of these interactions will improve current force-fields, and help understand structural motifs containing these residues.
Roya Momen - One of the best experts on this subject based on the ideXlab platform.
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the role of weak interactions in characterizing peptide folding preferences using a qtaim interpretation of the Ramachandran Plot ϕ ψ
International Journal of Quantum Chemistry, 2018Co-Authors: Roya Momen, Sergei Manzhos, Alireza Azizi, Steven R Kirk, Lingling Wang, Ping Yang, Samantha JenkinsAbstract:The original Ramachandran Plot is a potent way to understand structures of biomolecules, however only backbone conformations are considered. We formulate a new interpretation of the original Ramachandran Plot (ϕ-ψ) that can include a description of the weaker interactions including both the hydrogen bonds and HH bonds as a new way to derive insights into the phenomenon of peptide folding. Specifically, we show that QTAIM analysis permits identifying key regions of the Ramachandran Plot without the need for massive data sets. The QTAIM interpreted Ramachandran Plot is derived from QTAIM eigenvectors and not a trivial coordinate transformation. An investigation of both the backbone and the weaker bonds within the framework of the QTAIM interpreted Ramachandran Plot was found to be in line with physical intuition. The least-preferred directions calculated for the hydrogen bonds and HH bonds were found to coincide with the “unlikely” regions of the Ramachandran Plot.
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Exploration of the forbidden regions of the Ramachandran Plot (ϕ-ψ) with QTAIM
Physical Chemistry Chemical Physics, 2017Co-Authors: Roya Momen, Tianlv Xu, Wenxuan Li, Sergei Manzhos, Alireza Azizi, Steven R Kirk, Lingling Wang, Yang Ping, Samantha JenkinsAbstract:A new QTAIM interpretation of the Ramachandran Plot is formulated from the most and least facile eigenvectors of the second-derivative matrix of the electron density with a set of 29 magainin-2 peptide conformers. The presence of QTAIM eigenvectors associated with the most and least preferred directions of electronic charge density explained the role of hydrogen bonding, H⋯H contacts and the glycine amino acid monomer in peptide folding. The highest degree of occupation of the QTAIM interpreted Ramachandran Plot was found for the glycine amino acid monomer compared with the remaining backbone peptide bonds. The mobility of the QTAIM eigenvectors of the glycine amino acid monomer was higher than for the other amino acids and was comparable to that of the hydrogen bonding, explaining the flexibility of the magainin-2 backbone. We experimented with a variety of hybrid QTAIM–Ramachandran Plots to highlight and explain why the glycine amino acid monomer largely occupies the ‘forbidden’ region on the Ramachandran Plot. In addition, the new hybrid QTAIM–Ramachandran Plots contained recognizable regions that can be associated with concepts familiar from the conventional Ramachandran Plot whilst retaining the character of the QTAIM most and least preferred regions.
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The Role of Weak Interactions in Characterizing Peptide Folding Preferences using a QTAIM Interpretation of the Ramachandran Plot ({\phi}-{\psi})
International Journal of Quantum Chemistry, 2017Co-Authors: Roya Momen, Sergei Manzhos, Alireza Azizi, Steven R Kirk, Lingling Wang, Yang Ping, Samantha JenkinsAbstract:The Ramachandran Plot is a potent way to understand structures of biomolecules, however, the original formulation of the Ramachandran Plot only considers backbone conformations. We formulate a new interpretation of the original Ramachandran Plot ($\phi-\psi$) that can include a description of the weaker interactions including both the hydrogen bonds and H$---$H bonds as a new way to derive insights into the phenomenon of peptide folding. We use QTAIM (quantum theory of atoms in molecules) to interpret the Ramachandran Plot. Specifically, we show that QTAIM analysis permits identifying key regions of the Ramachandran Plot without the need for massive data sets. A highly non-linear relationship is found between the QTAIM vector-derived interpreted Ramachandran Plot and the conventional Ramachandran Plot ($\phi-\psi$) demonstrating that this new approach is not a trivial coordinate transformation. An investigation of both the backbone and the weaker bonds within the framework of the QTAIM interpreted Ramachandran Plot was found to be in line with physical intuition. The least-preferred directions calculated for the hydrogen bonds and H$---$H bonds were found to coincide with the 'unlikely' regions of the Ramachandran Plot.
Vladimir G. Tumanyan - One of the best experts on this subject based on the ideXlab platform.
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Descriptive statistics of disallowed regions and various protein secondary structures in the context of studying twisted β-hairpins
Biophysics, 2016Co-Authors: I. Yu. Torshin, N. G. Esipova, L. A. Uroshlev, Vladimir G. TumanyanAbstract:A detailed analysis of polypeptide-chain backbone conformations was carried out for polypeptide-chain segments adjacent to β-turn regions, including the sites of disallowed conformations. A cross comparison of conformations was performed for disallowed regions of the Ramachandran Plot and main types of β-turns and adjacent secondary structures. Based on the results, disallowed region 2 (II, II') in the Ramachandran Plot was shown to coincide mainly with β-hairpins and, more exactly, twisted β-hairpins. The frequency of residues with angles ϕ i , ψ i that fall in region 2 (II, II') in the latter is 140 times higher than in common β-hairpins.
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Alternatingly twisted β-hairpins and nonglycine residues in the disallowed II' region of the Ramachandran Plot.
Journal of biomolecular structure & dynamics, 2013Co-Authors: Ivan Yu. Torshin, N. G. Esipova, Vladimir G. TumanyanAbstract:The structure of the SH3 domain of α-spectrin (PDB code 1SHG) features Asn47 in the II′ area of the Ramachandran Plot, which as a rule admits only glycine residues, and this phenomenon still awaits its explanation. Here, we undertook a computational study of this particular case by means of molecular dynamics and bioinformatics approaches. We found that the region of the SH3 domain in the vicinity of Asn47 remains relatively stable during denaturing molecular dynamics simulations of the entire domain and of its parts. This increased stability may be connected with the dynamic hydrogen bonding that is susceptible to targeted in silico mutations of Arg49. Bioinformatics analysis indicated that Asn47 is in the β-turn of a distinctive structural fragment we called ‘alternatingly twisted β-hairpin.’ Fragments of similar conformation are quite abundant in a nonredundant set of PDB chains and are distinguished from ordinary β-hairpins by some surplus of glycine in their β-turns, lack of certain interpeptide hydr...
Sergei Manzhos - One of the best experts on this subject based on the ideXlab platform.
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the role of weak interactions in characterizing peptide folding preferences using a qtaim interpretation of the Ramachandran Plot ϕ ψ
International Journal of Quantum Chemistry, 2018Co-Authors: Roya Momen, Sergei Manzhos, Alireza Azizi, Steven R Kirk, Lingling Wang, Ping Yang, Samantha JenkinsAbstract:The original Ramachandran Plot is a potent way to understand structures of biomolecules, however only backbone conformations are considered. We formulate a new interpretation of the original Ramachandran Plot (ϕ-ψ) that can include a description of the weaker interactions including both the hydrogen bonds and HH bonds as a new way to derive insights into the phenomenon of peptide folding. Specifically, we show that QTAIM analysis permits identifying key regions of the Ramachandran Plot without the need for massive data sets. The QTAIM interpreted Ramachandran Plot is derived from QTAIM eigenvectors and not a trivial coordinate transformation. An investigation of both the backbone and the weaker bonds within the framework of the QTAIM interpreted Ramachandran Plot was found to be in line with physical intuition. The least-preferred directions calculated for the hydrogen bonds and HH bonds were found to coincide with the “unlikely” regions of the Ramachandran Plot.
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Exploration of the forbidden regions of the Ramachandran Plot (ϕ-ψ) with QTAIM
Physical Chemistry Chemical Physics, 2017Co-Authors: Roya Momen, Tianlv Xu, Wenxuan Li, Sergei Manzhos, Alireza Azizi, Steven R Kirk, Lingling Wang, Yang Ping, Samantha JenkinsAbstract:A new QTAIM interpretation of the Ramachandran Plot is formulated from the most and least facile eigenvectors of the second-derivative matrix of the electron density with a set of 29 magainin-2 peptide conformers. The presence of QTAIM eigenvectors associated with the most and least preferred directions of electronic charge density explained the role of hydrogen bonding, H⋯H contacts and the glycine amino acid monomer in peptide folding. The highest degree of occupation of the QTAIM interpreted Ramachandran Plot was found for the glycine amino acid monomer compared with the remaining backbone peptide bonds. The mobility of the QTAIM eigenvectors of the glycine amino acid monomer was higher than for the other amino acids and was comparable to that of the hydrogen bonding, explaining the flexibility of the magainin-2 backbone. We experimented with a variety of hybrid QTAIM–Ramachandran Plots to highlight and explain why the glycine amino acid monomer largely occupies the ‘forbidden’ region on the Ramachandran Plot. In addition, the new hybrid QTAIM–Ramachandran Plots contained recognizable regions that can be associated with concepts familiar from the conventional Ramachandran Plot whilst retaining the character of the QTAIM most and least preferred regions.
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The Role of Weak Interactions in Characterizing Peptide Folding Preferences using a QTAIM Interpretation of the Ramachandran Plot ({\phi}-{\psi})
International Journal of Quantum Chemistry, 2017Co-Authors: Roya Momen, Sergei Manzhos, Alireza Azizi, Steven R Kirk, Lingling Wang, Yang Ping, Samantha JenkinsAbstract:The Ramachandran Plot is a potent way to understand structures of biomolecules, however, the original formulation of the Ramachandran Plot only considers backbone conformations. We formulate a new interpretation of the original Ramachandran Plot ($\phi-\psi$) that can include a description of the weaker interactions including both the hydrogen bonds and H$---$H bonds as a new way to derive insights into the phenomenon of peptide folding. We use QTAIM (quantum theory of atoms in molecules) to interpret the Ramachandran Plot. Specifically, we show that QTAIM analysis permits identifying key regions of the Ramachandran Plot without the need for massive data sets. A highly non-linear relationship is found between the QTAIM vector-derived interpreted Ramachandran Plot and the conventional Ramachandran Plot ($\phi-\psi$) demonstrating that this new approach is not a trivial coordinate transformation. An investigation of both the backbone and the weaker bonds within the framework of the QTAIM interpreted Ramachandran Plot was found to be in line with physical intuition. The least-preferred directions calculated for the hydrogen bonds and H$---$H bonds were found to coincide with the 'unlikely' regions of the Ramachandran Plot.