Effect of D to E mutation of the RGD motif in rhodostomin on its activity, structure, and dynamics: Importance of the interactions between the D residue and integrin

Chiu Yueh Chen, Jia Hau Shiu, Yao Husn Hsieh, Yu Chen Liu, Yen Chin Chen, Yi Chun Chen, Wen Yih Jeng, Ming Jer Tang, Szecheng J. Lo, Woei Jer Chuang

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Abstract

Rhodostomin (Rho) is a snake venom protein containing an RGD motif that specifically inhibits the integrin-binding function. Rho produced in Pichia pastoris inhibits platelet aggregation with a K I of 78 nM as potent as native Rho. In contrast, its D51E mutant inhibits platelet aggregation with a K I of 49 μM. Structural analysis of Rho and its D51E mutant showed that they have the same tertiary fold with three twostranded antiparallel β-sheets. There are no structural backbone differences between the RG[D/E] loop which extends outward from the protein core and the RG[D/E] sequence at its apex in a four-residue RG[D/E]M type I turn. Two minor differences between Rho and its D51E mutant were only found from their backbone dynamics and 3D structures. The R 2 value of E51 is 13% higher than that of the D51 residue. A difference in the charge separation of 1.76 Å was found between the sidechains of positive (R49) and negative residues (D51 or E51).The docking of Rho into integrin αvβ3 showed that the backbone amide and carbonyl groups of the D51 residue of Rho were formed hydrogen bonds with the integrin residues R216 and R214, respectively. In contrast, these hydrogen bonds were absent in the D51E mutantintegrin complex. Our findings suggest that the interactions between both the sidechain and backbone of the D residue of RGD-containing ligands and integrin are important for their binding.

Original languageEnglish
Pages (from-to)808-821
Number of pages14
JournalProteins: Structure, Function and Bioinformatics
Volume76
Issue number4
DOIs
Publication statusPublished - 2009 Sep 1

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Integrins
Mutation
Platelets
Platelet Aggregation
Hydrogen
Hydrogen bonds
Agglomeration
Snake Venoms
Pichia
rhodostomin
Amides
Structural analysis
Proteins
Ligands

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry
  • Molecular Biology

Cite this

@article{4071aac9f81d43b89134d6067b7d18c4,
title = "Effect of D to E mutation of the RGD motif in rhodostomin on its activity, structure, and dynamics: Importance of the interactions between the D residue and integrin",
abstract = "Rhodostomin (Rho) is a snake venom protein containing an RGD motif that specifically inhibits the integrin-binding function. Rho produced in Pichia pastoris inhibits platelet aggregation with a K I of 78 nM as potent as native Rho. In contrast, its D51E mutant inhibits platelet aggregation with a K I of 49 μM. Structural analysis of Rho and its D51E mutant showed that they have the same tertiary fold with three twostranded antiparallel β-sheets. There are no structural backbone differences between the RG[D/E] loop which extends outward from the protein core and the RG[D/E] sequence at its apex in a four-residue RG[D/E]M type I turn. Two minor differences between Rho and its D51E mutant were only found from their backbone dynamics and 3D structures. The R 2 value of E51 is 13{\%} higher than that of the D51 residue. A difference in the charge separation of 1.76 {\AA} was found between the sidechains of positive (R49) and negative residues (D51 or E51).The docking of Rho into integrin αvβ3 showed that the backbone amide and carbonyl groups of the D51 residue of Rho were formed hydrogen bonds with the integrin residues R216 and R214, respectively. In contrast, these hydrogen bonds were absent in the D51E mutantintegrin complex. Our findings suggest that the interactions between both the sidechain and backbone of the D residue of RGD-containing ligands and integrin are important for their binding.",
author = "Chen, {Chiu Yueh} and Shiu, {Jia Hau} and Hsieh, {Yao Husn} and Liu, {Yu Chen} and Chen, {Yen Chin} and Chen, {Yi Chun} and Jeng, {Wen Yih} and Tang, {Ming Jer} and Lo, {Szecheng J.} and Chuang, {Woei Jer}",
year = "2009",
month = "9",
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TY - JOUR

T1 - Effect of D to E mutation of the RGD motif in rhodostomin on its activity, structure, and dynamics

T2 - Importance of the interactions between the D residue and integrin

AU - Chen, Chiu Yueh

AU - Shiu, Jia Hau

AU - Hsieh, Yao Husn

AU - Liu, Yu Chen

AU - Chen, Yen Chin

AU - Chen, Yi Chun

AU - Jeng, Wen Yih

AU - Tang, Ming Jer

AU - Lo, Szecheng J.

AU - Chuang, Woei Jer

PY - 2009/9/1

Y1 - 2009/9/1

N2 - Rhodostomin (Rho) is a snake venom protein containing an RGD motif that specifically inhibits the integrin-binding function. Rho produced in Pichia pastoris inhibits platelet aggregation with a K I of 78 nM as potent as native Rho. In contrast, its D51E mutant inhibits platelet aggregation with a K I of 49 μM. Structural analysis of Rho and its D51E mutant showed that they have the same tertiary fold with three twostranded antiparallel β-sheets. There are no structural backbone differences between the RG[D/E] loop which extends outward from the protein core and the RG[D/E] sequence at its apex in a four-residue RG[D/E]M type I turn. Two minor differences between Rho and its D51E mutant were only found from their backbone dynamics and 3D structures. The R 2 value of E51 is 13% higher than that of the D51 residue. A difference in the charge separation of 1.76 Å was found between the sidechains of positive (R49) and negative residues (D51 or E51).The docking of Rho into integrin αvβ3 showed that the backbone amide and carbonyl groups of the D51 residue of Rho were formed hydrogen bonds with the integrin residues R216 and R214, respectively. In contrast, these hydrogen bonds were absent in the D51E mutantintegrin complex. Our findings suggest that the interactions between both the sidechain and backbone of the D residue of RGD-containing ligands and integrin are important for their binding.

AB - Rhodostomin (Rho) is a snake venom protein containing an RGD motif that specifically inhibits the integrin-binding function. Rho produced in Pichia pastoris inhibits platelet aggregation with a K I of 78 nM as potent as native Rho. In contrast, its D51E mutant inhibits platelet aggregation with a K I of 49 μM. Structural analysis of Rho and its D51E mutant showed that they have the same tertiary fold with three twostranded antiparallel β-sheets. There are no structural backbone differences between the RG[D/E] loop which extends outward from the protein core and the RG[D/E] sequence at its apex in a four-residue RG[D/E]M type I turn. Two minor differences between Rho and its D51E mutant were only found from their backbone dynamics and 3D structures. The R 2 value of E51 is 13% higher than that of the D51 residue. A difference in the charge separation of 1.76 Å was found between the sidechains of positive (R49) and negative residues (D51 or E51).The docking of Rho into integrin αvβ3 showed that the backbone amide and carbonyl groups of the D51 residue of Rho were formed hydrogen bonds with the integrin residues R216 and R214, respectively. In contrast, these hydrogen bonds were absent in the D51E mutantintegrin complex. Our findings suggest that the interactions between both the sidechain and backbone of the D residue of RGD-containing ligands and integrin are important for their binding.

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U2 - 10.1002/prot.22387

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