Conformations of proline

DeTar, DeLos F.; Luthra, Narender P.

doi:10.1021/ja00446a040

Cited by 207 publications

(120 citation statements)

References 29 publications

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“…In fact, DeTar and Luthra had already utilized χ 2 as one of the parameters in describing proline puckering. 8 In our study, we find that the χ 2 -puckering pathway is linearly correlated with the puckering amplitude q m (Figs. 6-8), and it changes more symmetrically with the phase angle p m (Figs.…”

Section: Discussionsupporting

confidence: 58%

“…And this was also noticed by DeTar and Luthra. 8 To compare with the puckering pathway along the φ angle described by the pseudorotation phase angle and amplitude, we plot φ-p m and φ-q m calculated by the gas-phase and aqueous-phase simulations, and also by the PDB-structure analyses. We present the results in Fig.…”

Section: E Proline Puckering Along the Backbone Torsion Angle φmentioning

confidence: 99%

“…The graphs are visualized using Chimera. 38 As an important and special feature of proline, the pyrrolidine ring puckering has been studied in detail, 4,[8][9][10][11][12][13][14][15][16][17] and proline's two preferred puckering states have been characterized very well. Usually, the pyrrolidine ring puckering is symbolized with two parameters-the pseudorotation phase angle and amplitude-that can be calculated either by the five ring-atom positions 18 or by the five endocyclic torsion angles χ j .…”

Section: Introductionmentioning

confidence: 99%

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The puckering free-energy surface of proline

2013

AIP Advances

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Proline has two preferred puckering states, which are often characterized by the pseudorotation phase angle and amplitude. Although proline's five endocyclic torsion angles can be utilized to calculate the phase angle and amplitude, it is not clear if there is any direct correlation between each torsion angle and the proline-puckering pathway. Here we have designed five proline puckering pathways utilizing each torsion angle χj (j = 1∼5) as the reaction coordinate. By examining the free-energy surfaces of the five puckering pathways, we find they can be categorized into two groups. The χ2 pathway (χ2 is about the Cβ—Cγ bond) is especially meaningful in describing proline puckering: it changes linearly with the puckering amplitude and symmetrically with the phase angle. Our results show that this conclusion applies to both trans and cis proline conformations. We have also analyzed the correlations of proline puckering and its backbone torsion angles ϕ and ψ. We show proline has preferred puckering states at the specific regions of ϕ, ψ angles. Interestingly, the shapes of ψ-χ2 free-energy surfaces are similar among the trans proline in water, cis proline in water and cis proline in the gas phase, but they differ substantially from that of the trans proline in the gas phase. Our calculations are conducted using molecular simulations; we also verify our results using the proline conformations selected from the Protein Data Bank. In addition, we have compared our results with those calculated by the quantum mechanical methods

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Section: Discussionsupporting

confidence: 58%

Section: E Proline Puckering Along the Backbone Torsion Angle φmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The puckering free-energy surface of proline

2013

AIP Advances

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“…Peptides containing proline residues have been the subject of intensive study because of the possibility of cis-trans isomerization about the X-Pro bond (Carver & Blout, 1976;Grathwohl & Wuthrich, 1976), variations in pyrrolidine-ring geometries (Detar & Luthra, 1977;Madison, 1977) and the widespread occurrence of Pro residues in proteins. 0567-7408/82/010172-05501.00…”

Section: Introductionmentioning

confidence: 99%

Structure of tert-butyloxycarbonyl-L-alanyl-L-proline monohydrate (t-Boc-Ala-Pro)

Kamwaya¹,

Oster²,

Bradaczek³

et al. 1982

Acta Crystallogr Sect B

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“…The two pyrrolidine rings are in envelope conformations with C(4) and C(9) atoms out of the least-squares planes of the other four atoms of the respective rings. The conformation of these rings may also be described using the conformational equations of DeTar & Luthra (1977). According to these authors, the ith torsional angle in the five-membered ring is given by the equation Xi = a0 cos[t + 4z~(i -2)/5], where a 0 is the puckering amplitude and t is the phase angle.…”

mentioning

confidence: 99%