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4-羟基-L-脯氨酸异构体对无鸟氨酸短杆菌肽S构象的褶皱效应

Puckering effects of 4-hy-droxy-l-proline isomers on the conformation of ornithine-free Gramicidin S.

作者信息

Asano Akiko, Nakayama Kanako, Okada Sakura, Kato Takuma, Doi Mitsunobu

机构信息

Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 590-1094, Japan.

出版信息

Acta Crystallogr E Crystallogr Commun. 2024 Aug 9;80(Pt 9):942-946. doi: 10.1107/S2056989024007771. eCollection 2024 Sep 1.

DOI:10.1107/S2056989024007771
PMID:39267874
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11389682/
Abstract

The cyclic peptide (Val-Leu-Leu-d-Phe-Pro) (peptide ) was specifically designed for structural chemistry investigations, drawing inspiration from Gramicidin S (GS). Previous studies have shown that Pro residues within adopt a down-puckering conformation of the pyrrolidine ring. By incorporating fluoride-Pro with 4-/-isomers into , an up-puckering conformation was successfully induced. In the current investigation, introducing hy-droxy-prolines with 4-/-isomer configurations (tHyp/cHyp) into gave (Val-Leu-Leu-d-Phe-tHyp) methanol disolvate monohydrate, CHNO·2CHO·HO (), and (Val-Leu-Leu-d-Phe-cHyp) monohydrate, CHNO·HO (), respectively. However, the puckering of and remained in the down conformation, regardless of the geometric position of the hydroxyl group. Although the backbone structure of with -substitution was asymmetric, the asymmetric backbone of with -substitution was unexpected. It is speculated that the anti-cipated influence of stress from the geometric positioning, which was expected to affect the puckering, may have been mitigated by inter-actions between the hydroxyl groups of hy-droxy-proline, the solvent mol-ecules, and peptides.

摘要

环肽(Val-Leu-Leu-d-Phe-Pro)(肽 )是专门为结构化学研究设计的,灵感来源于短杆菌肽S(GS)。先前的研究表明, 中的Pro残基采用吡咯烷环的下皱构象。通过将具有4 - / - 异构体的氟代-Pro引入 ,成功诱导了上皱构象。在当前研究中,将具有4 - / - 异构体构型(tHyp/cHyp)的羟基脯氨酸引入 分别得到了甲醇溶剂化物一水合物(Val-Leu-Leu-d-Phe-tHyp),CHNO·2CHO·HO( )和一水合物(Val-Leu-Leu-d-Phe-cHyp),CHNO·HO( )。然而,无论羟基的几何位置如何, 和 的皱折仍保持在下构象。尽管具有 - 取代的 的主链结构是不对称的,但具有 - 取代的 的不对称主链是出乎意料的。据推测,预期会影响皱折的几何定位应力的预期影响可能已通过羟基脯氨酸的羟基、溶剂分子和肽之间的相互作用得到缓解。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/13cf/11389682/915a822d4f32/e-80-00942-fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/13cf/11389682/94786ff78a56/e-80-00942-fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/13cf/11389682/05f8ec375857/e-80-00942-fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/13cf/11389682/d0c8b4b7ae20/e-80-00942-fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/13cf/11389682/e95e3399e292/e-80-00942-fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/13cf/11389682/915a822d4f32/e-80-00942-fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/13cf/11389682/94786ff78a56/e-80-00942-fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/13cf/11389682/05f8ec375857/e-80-00942-fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/13cf/11389682/d0c8b4b7ae20/e-80-00942-fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/13cf/11389682/e95e3399e292/e-80-00942-fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/13cf/11389682/915a822d4f32/e-80-00942-fig5.jpg

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本文引用的文献

1
An Ornithine-Free Gramicidin S Analogue Using Norleucine, Cyclo(Val-Nle-Leu-D-Phe-Pro), Forms Helically Aligned β-Sheets.一种使用正亮氨酸的无鸟氨酸短杆菌肽 S 类似物,环(缬氨酸-正亮氨酸-亮氨酸-D-苯丙氨酸-脯氨酸),形成螺旋排列的β-折叠片层。
Chem Pharm Bull (Tokyo). 2021;69(11):1097-1103. doi: 10.1248/cpb.c21-00548.
2
validation ALERTS: what they mean and how to respond.验证警报:其含义及应对方法
Acta Crystallogr E Crystallogr Commun. 2020 Jan 1;76(Pt 1):1-11. doi: 10.1107/S2056989019016244.
3
[Leu]Gramicidin S preserves the structural properties of its parent peptide and forms helically aligned β-sheets.
[亮氨酸]短杆菌肽S保留了其母肽的结构特性,并形成螺旋排列的β-折叠片。
Acta Crystallogr C Struct Chem. 2019 Oct 1;75(Pt 10):1336-1343. doi: 10.1107/S2053229619011872. Epub 2019 Sep 6.
4
Use of intensity quotients and differences in absolute structure refinement.强度商数的使用及绝对结构精修中的差异
Acta Crystallogr B Struct Sci Cryst Eng Mater. 2013 Jun;69(Pt 3):249-59. doi: 10.1107/S2052519213010014. Epub 2013 May 17.
5
Antimicrobially active cycloundecapeptides related to gramicidin S having a novel turn structure with cis D-Phe-Pro peptide bond.具有新型顺式 D-Phe-Pro 肽键的结构的、与短杆菌肽 S 相关的具有抗菌活性的环十一肽。
Org Biomol Chem. 2010 Apr 21;8(8):1791-7. doi: 10.1039/b922159j.
6
Double-stranded helical twisted beta-sheet channels in crystals of gramicidin S grown in the presence of trifluoroacetic and hydrochloric acids.在三氟乙酸和盐酸存在下生长的短杆菌肽S晶体中的双链螺旋扭曲β-折叠通道。
Acta Crystallogr D Biol Crystallogr. 2007 Mar;63(Pt 3):401-7. doi: 10.1107/S0907444906056435. Epub 2007 Feb 21.
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Possible molecular models for gramicidin S and their relationship to present ideas of protein structure.短杆菌肽S可能的分子模型及其与当前蛋白质结构观点的关系。
Biochem J. 1957 Apr;65(4):752-6. doi: 10.1042/bj0650752.
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A crystallographic study of some derivatives of gramicidin S.短杆菌肽S某些衍生物的晶体学研究
Biochem J. 1957 Apr;65(4):744-50. doi: 10.1042/bj0650744.
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Antiparallel pleated beta-sheets observed in crystal structures of N,N-bis(trichloroacetyl) and N,N-bis(m-bromobenzoyl) gramicidin S.在N,N-双(三氯乙酰基)和N,N-双(间溴苯甲酰基)短杆菌肽S的晶体结构中观察到的反平行β-折叠片层
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