Pyrrolidine ring puckering in cis and trans-proline residues in proteins and polypeptides

Milner‐White, E. James; Bell, Lachlan H.; Maccallum, Peter H.

doi:10.1016/0022-2836(92)90859-i

Cited by 143 publications

(145 citation statements)

References 25 publications

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“…Proline ring puckers can be defined by the torsion angles χ 1 i , χ 2 i , χ 3 i and χ 4 i (see caption to Fig. 4); alternatively, use can be made of the fact that the value of χ 1 i alone is indicative of the two major pucker forms [38] (Fig. 4). …”

Section: Specification Of Turns Disulfide Bonds and Proline Ringsmentioning

confidence: 99%

“…Typical values for the torsion angles also depend on whether the XxxϪPro peptide bond is cis or trans. Average values (in degrees) found from a number of X-ray structures of proteins for χ 1 , χ 2 , χ 3 , χ 4 were [38]: trans DOWN, 18, Ϫ29, 17, Ϫ4 ; cis DOWN, 26, Ϫ38, 18, Ϫ7; trans UP, Ϫ27, 35, Ϫ34, 20 ; cis UP, Ϫ21, 36, Ϫ36, 17. 6.…”

Section: Sugar Pucker: Torsion Angles and Angle Of Pseudorotationmentioning

confidence: 99%

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Recommendations for the presentation of NMR structures of proteins and nucleic acids

Markley

Bax

Arata³

et al. 1998

European Journal of Biochemistry

242

255

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The recommendations presented here are designed to support easier communication of NMR data and NMR structures of proteins and nucleic acids through unified nomenclature and reporting standards. Much of this document pertains to the reporting of data in journal articles; however, in the interest of the future development of structural biology, it is desirable that the bulk of the reported information be stored in computer-accessible form and be freely accessible to the scientific community in standardized formats for data exchange. These recommendations stem from an IUPAC-IUBMB-IUPAB inter-union venture with the direct involvement of ICSU and CODATA. The Task Group has reviewed previous formal recommendations and has extended them in the light of more recent developments in the field of biomolecular NMR spectroscopy. Drafts of the recommendations presented here have been examined critically by more than 50 specialists in the field and have gone through two rounds of extensive modification to incorporate suggestions and criticisms.

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Section: Specification Of Turns Disulfide Bonds and Proline Ringsmentioning

confidence: 99%

Section: Sugar Pucker: Torsion Angles and Angle Of Pseudorotationmentioning

confidence: 99%

Recommendations for the presentation of NMR structures of proteins and nucleic acids

Markley

Bax

Arata³

et al. 1998

European Journal of Biochemistry

242

255

View full text Add to dashboard Cite

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“…The prolyl residue has a fivemembered ring, which may adopt two distinct down-and up-puckered conformations that are almost equally favorable. 24,25,27,[34][35][36]40,43,46,47 Although the correlations of the cis/trans population and the prolyl puckering were suggested by analyzing X-ray structures of peptides and proteins, [48][49][50] it was known that the cisÀtrans isomerization and the puckering transition is not coupled and that the prolyl ring can flip between the down-and up-puckered conformations either with the trans or with the cis peptide bond. [35][36][37]43,47 There are a limited number of works that report on the conformational preferences of the Dhp residue.…”

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confidence: 99%

Conformational preferences and cis–trans isomerization of L‐3,4‐dehydroproline residue

Kang

Park

2009

Biopolymers

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The conformational study of N-acetyl-N'-methylamide of L-3,4-dehydroproline (Ac-Dhp-NHMe, the Dhp dipeptide) is carried out using hybrid density functional methods with the self-consistent reaction field method in the gas phase and in solution (chloroform and water). The incorporation of a double bond between C(beta) and C(gamma) into the prolyl ring results in the puckering, backbone population, and barriers to prolyl cis-trans isomerization different from those of the Pro dipeptide. For local minima of the Dhp dipeptide in the gas phase and in water, the C(beta)-C(gamma) bonds become shorter by approximately 0.2 A and the bond angles C(alpha)-C(beta)-C(gamma) and C(beta)-C(gamma)-C(delta) are widened by approximately 8 degrees than those of the Pro dipeptide, and the puckering amplitude is computed to be 0.01-0.07 A, indicating that the 3,4-dehydroprolyl ring is quite less puckered. However, polyproline-like conformations become preferred and the relative stability of the conformation tC with a C(7) intramolecular hydrogen bond decreases as the solvent polarity increases, as found for the Pro dipeptide. The barriers to cis-trans isomerization of the Ac-Dhp peptide bond increase with the increase of solvent polarity and the isomerization is likely to proceed through the clockwise rotation in water, as found for the prolyl peptide bond. The hydrogen bond between the prolyl nitrogen and the following amide N-H group seems to contribute in stabilizing the transition state structures.

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“…Proline is the only natural amino acid that contains a secondary amino group as part of a flexible five-membered ring. A number of experimental studies on the structure of the proline have been conducted in the condensed phase; [26][27][28] these studies include an x-ray diffraction analysis of the zwitterionic ring conformation, because of the high melting point of proline and associated low-vapor pressure. To date, no experimental structure of neutral proline has been reported.…”

Section: Resultsmentioning

confidence: 99%

Interaction of Proline with Cu⁺and Cu²⁺Ions in the Gas PhaseGab Yong Lee*Department of Life Chemistry, Catholic University of Daegu, Gyeongsan 712‐702, Korea(Received March 3, 2009)INTRODUCTIONCopper ions are the most important transitionmetals involved in several biological processes ofliving systems, including oxidation, dioxygentransport, and charge transfer.1 The study of interactionsbetween the metal ion and amino acids hasattracted considerable attention from experimental2-6and

Lee¹

2009

Journal of the Korean Chemical Society

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Pyrrolidine ring puckering in cis and trans-proline residues in proteins and polypeptides

Cited by 143 publications

References 25 publications

Recommendations for the presentation of NMR structures of proteins and nucleic acids

Recommendations for the presentation of NMR structures of proteins and nucleic acids

Conformational preferences and cis–trans isomerization of L‐3,4‐dehydroproline residue

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