Structure of cyclo-(L-threonyl-D-valyl-L-prolyl-sarcosyl-N-methyl-L-valyl-OThr) at 153 K

Pohl, Ehmke; Sheldrick, George M.; Fischer, Sebastian Nils; Lackner, Helmut

doi:10.1107/s0108270193007334

Cited by 5 publications

(4 citation statements)

References 10 publications

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“…95 little structural information is available for bioactive pseudopeptide analogues. 95 little structural information is available for bioactive pseudopeptide analogues.…”

Section: Figure 16mentioning

confidence: 99%

“…and 11, cyclo -( Gly-Tyr-Gly-Pro-Leu-Pro) , isolated from Clerodendrum myricoides, has not been e~tablished.~~ The crystal structure of the latter in the trihydrate form has been recently solved by Declercq et al,94 and the conformation of the molecule essentially consists of two turns of the PI1 ( Pro-Gly sequence) and PII' (Gly-Pro sequence) types with the two Tyr-NH to Leu-CO ( N . The crystal structure of the isolated pentapeptide lactone cyclo ( Thr-D-Val-Pro-Sar-N-Me-L-Val-O,,,) has been solved recently by Sheldrick's group(Figure 16) 95. .O = 2.94 A) and Leu-NH to Tyr-CO ( N .…”

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confidence: 99%

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Crystal structures of peptides and modified peptides

Marraud

Aubry

1996

Biopolymers

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The X‐ray diffraction experiments on peptides and related molecules which have been carried out in Western Europe, except Italy, in the last eight years are reviewed. The crystal structures of some bioactive peptides such as Leu‐enkephalin (a neurotransmitter), cyclosporin A (an immunomodulator in both the free and protein‐bound state), balhimycin (an antibiotic) and octreotide (a somatostatin analogue) are briefly presented. Crystallized N‐ and C‐protected model peptides have given an insight into the folding tendency and folding modes depending on the peptide sequences. The crystal structures of various pseudopeptide molecules reveal how the three‐dimensional structure of peptide analogues can be modulated by substituting non‐peptide groups for the peptide bond. A few examples of structural mimetics of the β‐ and γ‐turns, and of templates for α‐helix induction are also presented. © 1996 John Wiley & Sons, Inc.

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“…95 little structural information is available for bioactive pseudopeptide analogues. 95 little structural information is available for bioactive pseudopeptide analogues.…”

Section: Figure 16mentioning

confidence: 99%

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confidence: 99%

Crystal structures of peptides and modified peptides

Marraud

Aubry

1996

Biopolymers

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“…It is found from the designing studies that the presence of d AA residues in the peptides enhances their stability and suppresses the protease activity. ,− The inhibition of protease activity may be due to less accessibility of peptide bonds formed by the d AAs when compared to the bonds formed by the l AAs. ,, Hence, several peptides containing d AA residues have been designed and synthesized. The biological activities of these heterochiral peptides, such as antimicrobial, antibacterial, and anticancer, have been determined using various experimental methods. − Computational modeling studies have also been undertaken to understand the biological activities of modified peptides. − …”

Section: Introductionmentioning

confidence: 99%

Molecular Dynamics Investigations on the Effect of d Amino Acid Substitution in a Triple-Helix Structure and the Stability of Collagen

et al. 2009

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Studies on the structure and stability of peptides and proteins during l-->d configurational change are certainly important for the designing of peptides with new biological activity and protein engineering. The l-->d amino acid (d AA) changes have been observed in aged proteins such as collagen. Hence, in this study, an attempt has been made to explore the effect of the replacement of l amino acid (l AA) in the model collagen-like peptides with d AA and the origin of structural stability (destability) has been traced using the molecular dynamics (MD) method employing the AMBER force field. Our results reveal that the substitution of d AA produces a large local disruption to the triple-helical structure. Formation of a kink (bulge) at the site of substitution is observed from the detailed analysis of MD trajectory. However, this local perturbation of kinked helix changes the direction of the helices and affects the relative orientation of the respective AA residues for helix-helix interaction, enough to affect the overall stability of the model collagen-like peptide. The destabilization energy per d Ala substitution is 7.87 kcal/mol, which is similar to the value for the Gly-->Ala mutation in collagen. Since the Gly-->Ala mutation is involved in genetic disorders such as osteogenesis imperfecta (OI), the l-->d configurational change may produce a similar effect on collagen.

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“…From a functional point of view, their unnatural stereochemistry often means that compounds containing D ‐residues are much more resistant to enzyme‐catalyzed breakdown than natural peptides, a property of considerable pharmaceutical and microbiologic importance. Indeed, a number of antibacterial and antitumor compounds contain D ‐amino acid residues 3, 4…”

Section: Introductionmentioning

confidence: 99%

D‐amino acid residues in peptides and proteins

Mitchell

Smith

2003

Proteins

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We have investigated the D-amino acid residues present in Protein Data Bank (PDB) entries, categorizing them into "real" D-residues and artifacts. In polypeptide chains of more than 20 residues, only a single instance of a "real" D-residue, other than those deliberately designed or engineered, was found. This example was the result of a slow chemical epimerization process. Another 12 designed D-residues were found in these longer polypeptide chains. Smaller peptides of 20 or fewer residues contained 479 "real" D-residues, the majority in various gramicidin, actinomycin, or cyclosporin structures. We found 148 PDB entries with "real" D-residues and a further 186, in which all apparent D-residues are artifacts. Investigating the (phi, psi) preferences of the "real" D-residues, we found that the region around (-60 degrees, -45 degrees ) was almost completely unoccupied, even though it is not formally disallowed. We link the low propensity to occupy this region with the alpha-helix destabilizing properties of D-residues.

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Structure of cyclo-(L-threonyl-D-valyl-L-prolyl-sarcosyl-N-methyl-L-valyl-OThr) at 153 K

Abstract: The crystal structure of cyclo-(n-Thr-D-Val-g-Pro-Sar-N-u-MeVal-OThr), C23H39N506.HC1.MeOH.H20 is reported. This cyclic pentapeptide lactone represents one

Cited by 5 publications

References 10 publications

Crystal structures of peptides and modified peptides

Crystal structures of peptides and modified peptides

Molecular Dynamics Investigations on the Effect of d Amino Acid Substitution in a Triple-Helix Structure and the Stability of Collagen

D‐amino acid residues in peptides and proteins

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