Coulombic interactions between partially charged main-chain atoms not hydrogen-bonded to each other influence the conformations of α-helices and antiparallel β-sheet. A new method for analysing the forces between hydrogen bonding groups in proteins includes all the Coulombic interactions

Maccallum, Peter H.; Poet, Ron; Milner‐White, E. James

doi:10.1016/s0022-2836(95)80056-5

Cited by 43 publications

(39 citation statements)

References 28 publications

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“…The self-contact between the side-chain and the main-chain C O groups reported in this study is different from the interactions of C O groups observed in earlier studies [6,18,[40][41][42]. In these studies, the partial positive charge of carbonyl carbon from one C O group has a favorable electrostatic interaction with the partial negative charge of carbonyl oxygen from another C O group.…”

Section: Discussioncontrasting

confidence: 99%

Self-contacts in Asx and Glx residues of high-resolution protein structures: Role of local environment and tertiary interactions

Pal

Sankararamakrishnan

2008

Journal of Molecular Graphics and Modelling

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Section: Discussioncontrasting

confidence: 99%

Self-contacts in Asx and Glx residues of high-resolution protein structures: Role of local environment and tertiary interactions

Pal

Sankararamakrishnan

2008

Journal of Molecular Graphics and Modelling

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“…Maccallum et al showed that a dipole interaction between CO–CO dipoles in proteins contributes as much to the direction of the twist in β-sheets as steric hindrance between side chains. 57,58 More recently, others showed that dipoles play a role in stabilizing various protein secondary structures by orienting them so that they are aligned with the external field created by the rest of the protein. 39 Our results may be compared to previous observations about the absence of H-bonds in studies on the collapse of longer, single oligoglycines 3,4 indicating that the same mechanism could be in effect in full-length unfolded, unordered proteins.…”

Section: Discussionmentioning

confidence: 99%

Solubility and Aggregation of Gly₅in Water

2014

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Experimentally, the solubility of oligoglycines in water decreases as its length increases. Computationally, the free energy of solvation becomes more favorable with chain length for short (n = 1–5) oligoglycines. We present results of large scale simulations with over 600 pentaglycines at varying concentrations in explicit solvent to consider the mechanism of aggregation. The solubility limit of Gly5 for the force field used was calculated and compared with experimental values. We find that intermolecular interactions between pentaglycines are favored over interactions between glycine and water, leading to their aggregation. However, the interaction driving peptide associations, liquid–liquid phase separation, are not predominantly hydrogen bonding. Instead, non-hydrogen bonding interactions between partially charged atoms on the peptide backbone allow the formation of dipole–dipole and charge layering correlations that mechanistically stabilize the formation of large, stable peptide clusters.

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“…The second discrepancy is that the Ramachandran plot cluster into distinct regions within the sterically-allowed regions of the Ramachandran plot [8,10]. These clusters have now been explained in terms of backbone dipole-dipole interactions [3,11,12]. …”

Section: Introductionmentioning

confidence: 99%

The Ramachandran plots of glycine and pre-proline

2005

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BackgroundThe 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.ResultsIn 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.ConclusionWe 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.

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Coulombic interactions between partially charged main-chain atoms not hydrogen-bonded to each other influence the conformations of α-helices and antiparallel β-sheet. A new method for analysing the forces between hydrogen bonding groups in proteins includes all the Coulombic interactions

Cited by 43 publications

References 28 publications

Self-contacts in Asx and Glx residues of high-resolution protein structures: Role of local environment and tertiary interactions

Self-contacts in Asx and Glx residues of high-resolution protein structures: Role of local environment and tertiary interactions

Solubility and Aggregation of Gly₅in Water

The Ramachandran plots of glycine and pre-proline

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Coulombic interactions between partially charged main-chain atoms not hydrogen-bonded to each other influence the conformations of α-helices and antiparallel β-sheet. A new method for analysing the forces between hydrogen bonding groups in proteins includes all the Coulombic interactions

Cited by 43 publications

References 28 publications

Self-contacts in Asx and Glx residues of high-resolution protein structures: Role of local environment and tertiary interactions

Self-contacts in Asx and Glx residues of high-resolution protein structures: Role of local environment and tertiary interactions

Solubility and Aggregation of Gly5in Water

The Ramachandran plots of glycine and pre-proline

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Solubility and Aggregation of Gly₅in Water