Occurrence and role ofcis peptide bonds in protein structures

Stewart, David E.; Sarkar, Atom; Wampler, John E.

doi:10.1016/0022-2836(90)90159-j

Cited by 513 publications

(454 citation statements)

References 41 publications

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“…As was calculated via published methods about 5% of all peptidyl-prolyl bonds known in the spatial structure are in the cis conformation in native proteins [15,16]. The trans to cis isomerization is often the rate limiting step during the refolding of polypeptides provided that there is a cis prolyl residue in the native state [8,17,18].…”

Section: Introductionmentioning

confidence: 99%

An 11.8 kDa proteolytic fragment of the E. coli trigger factor represents the domain carrying the peptidyl‐prolyl cis/trans isomerase activity

Stoller¹,

Tradler²,

Rücknagel³

et al. 1996

FEBS Letters

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The 48 kDa trigger factor (TF) of E. coli was shown to be a peptidyl-prolyl cisltrans isomerase (PPIase). Its location on a ribosomal particle is unique among the PPIases described so far, and suggests a role in de novo protein folding. The trigger factor was investigated with regard to a domain carrying the catalytic activity. An enzymatieally active fragment could be isolated after proteolysis by subtifisin. The resulting polypeptide was analysed by N-terminal sequencing and MALDI-TOF mass spectrometry revealing an 11.8 kDa fragment of TF encompassing the amino acid residues Arg-145 to Glu-251. The nucleotide sequence encoding the amino acid residues Met-140 to Ala-250 of the TF was cloned into vector pQE32. After expression in E. coli the resulting His-tagged polypeptide was isolated on an Ni 2+-NTA column. Subsequent digestion with subtifisin and anionexchange chromatography yielded a TF fragment encompassing amino acids Gin-148 to Thr-249. This fragment may represent the catalytic core of TF since PPIase activity with a specificity constant kcat/Km of 1.3 ~1-1 s -l could be demonstrated when using Suc-Ala-Phe-Pro-Phe-NH-Np as a substrate. Moreover, as was observed for the complete, authentic TF the PPIase activity of the fragment was not inhibited by the peptidomacrofide FK506.

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Section: Introductionmentioning

confidence: 99%

An 11.8 kDa proteolytic fragment of the E. coli trigger factor represents the domain carrying the peptidyl‐prolyl cis/trans isomerase activity

Stoller¹,

Tradler²,

Rücknagel³

et al. 1996

FEBS Letters

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“…'-space accessible to the peptide backbone becomes very limited. Compared to other amino acids, proline also appears more frequently in proteins with a cis peptide bond [3]. Proline residues thus have a special significance in their effect on chain conformation, which in turn can influence protein folding, and also peptide and protein function [4].…”

Section: Introductionmentioning

confidence: 99%

β‐Turns induced in bradykinin by (S)‐α‐methylproline

1992

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The ability of (S).g-methylprolin¢ (g-MePro) to stabilis¢ reversequrn conformations in the peptlde hormone brad~/kinin (BK = Argt-Pro:-ProLGly 4-PheS-Ser6-ProLPhe~-Arg ~) has been investigated. Two BK analogues containing ,)-MePro at position 3 or position 7 were synthesised and their conformations in aqueous solution investigated by NMR spectroscopy. Whereas BK is largely disordered on the NMR time scale both analogues showed ROE connectivities in 2D-ROESY spectra indicative of reverse-turn conformations at both Pro2-Phe ~ and Ser~-Arg °. whose formation appears to be cooperative. Some potential applications of ~z-McPro as a reverse-turn mimetic in the construction of synthetic peptide libraries is discussed.

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“…comm.). Although cis X-Pro peptide bonds occur commonly in folded proteins (6.5%, Stewart et al, 1990;MacArthur & Thornton, 1991), other cis peptide bonds are rare (0.05%, Stewart et al, 1990). Replacement of a cis proline residue necessarily produces either a cis nonproline peptide bond or else a change in backbone geometry (see Fig.…”

mentioning

confidence: 99%

Cis proline mutants of ribonuclease A. I. thermal stability

Schultz

Baldwin

1992

Protein Science

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A chemically synthesized gene for ribonuclease A has been expressed in Escherichia coli using a T7 expression system (Studier, F.W., Rosenberg, A.H., Dunn, J.J., & Dubendorff, J.W., 1990, Methods Enzymol. 185, 60-89). The expressed protein, which contains an additional N-terminal methionine residue, has physical and catalytic properties close to those of bovine ribonuclease A. The expressed protein accumulates in inclusion bodies and has scrambled disulfide bonds; the native disulfide bonds are regenerated during purification. Site-directed mutations have been made at each of the two cis proline residues, 93 and 114, and a double mutant has been made. In contrast to results reported for replacement of trans proline residues, replacement of either cis proline is strongly destabilizing. Thermal unfolding experiments on four single mutants give AT,,, e 10 "C and AAGo (apparent) = 2-3 kcal/mol. The reason is that either the substituted amino acid goes in cis, and cis H trans isomerization after unfolding pulls the unfolding equilibrium toward the unfolded state, or else there is a conformational change, which by itself is destabilizing relative to the wild-type conformation, that allows the substituted amino acid to form a trans peptide bond.

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Occurrence and role ofcis peptide bonds in protein structures

Cited by 513 publications

References 41 publications

An 11.8 kDa proteolytic fragment of the E. coli trigger factor represents the domain carrying the peptidyl‐prolyl cis/trans isomerase activity

An 11.8 kDa proteolytic fragment of the E. coli trigger factor represents the domain carrying the peptidyl‐prolyl cis/trans isomerase activity

β‐Turns induced in bradykinin by (S)‐α‐methylproline

Cis proline mutants of ribonuclease A. I. thermal stability

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