Rational Improvement of Peptide Affinity to Human Pregnancy-Related Serine Protease HtrA3 PDZ Domain by Introducing a Halogen Bond to the Domain–Peptide Complex Interface

Liu, Hong; Dou, Shuo-Fen; Zhao, Xue; Wang, Yan; Wen, Qingli; Mu, Yanan

doi:10.1007/s10989-016-9516-x

Cited by 10 publications

(6 citation statements)

References 21 publications

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“…It was found that halogen substitution at peptide Trp‐1 residue can form an effective halogen bond with HtrA1‐PDZ and HtrA3‐PDZ, which confers stability and specificity to the domain‐peptide recognition and association. Here, we systematically investigated the effect of all possible combination between the 4 halogen atoms (–F, –Cl, –Br, and –I) and 2 substitution positions (R2‐ and R4‐positions) at Trp‐1 indole ring on peptide affinity and selectivity to the 4 HtrA‐PDZs.…”

Section: Resultsmentioning

confidence: 99%

“…The peptide Ac– DSRIWWV –COOH as well as its 4 R2‐halogenated counterparts were prepared using Fmoc‐solid phase synthesis. The binding affinity between the PDZ and peptide was determined using fluorescence spectroscopy described previously . The fluorescence emission spectra of fluorescently active residues in the active site of HtrA1‐PDZ (residues 380‐480) were used to monitor peptide binding.…”

Section: Methodsmentioning

confidence: 99%

“…Previously, phage display technique has been widely used to identify short peptides with potential affinity to diverse PDZ domains, and several HtrA‐PDZ–peptide complex structures were also solved via solution NMR and X‐ray crystallography . Recently, Dou et al have successfully introduced halogen bonds at the complex interfaces of HtrA1‐PDZ and HtrA3‐PDZ with their cognate peptide ligands to improve affinity and specificity for the domain‐peptide interactions . It was found that different halogen atoms would shift the peptide selectivity subtly and exquisitely.…”

Section: Introductionmentioning

confidence: 99%

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Peptide selectivity between the PDZ domains of human pregnancy‐related serine proteases (HtrA1, HtrA2, HtrA3, and HtrA4) can be reshaped by different halogen probes

Sun

Wang

2017

J of Molecular Recognition

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The human HtrA family of serine proteases (HtrA1, HtrA2, HtrA3, and HtrA4) are the key enzymes associated with pregnancy and closely related to the development and progression of many pathological events. Previously, it was found that halogen substitution at the indole moiety of peptide Trp-1 residue can form a geometrically satisfactory halogen bond with the Drosophila discs large, zona occludens-1 (PDZ) domain of HtrA proteases. Here, we attempt to systematically investigate the effect of substitution with 4 halogen types and 2 indole positions on the binding affinity and specificity of peptide ligands to the 4 HtrA PDZ domains. The complex structures, interaction energies, halogen-bonding strength, and binding affinity of domain-peptide systems were modeled, analyzed, and measured via computational modeling and fluorescence-based assay. It is revealed that there is a compromise between the local rearrangement of halogen bond involving different halogen atoms and the global optimization of domain-peptide interaction; the substitution position is fundamentally important for peptide-binding affinity, while the halogen type can effectively shift peptide selectivity between the 4 domains. The HtrA1-PDZ and HtrA4-PDZ as well as HtrA2-PDZ and HtrA3-PDZ respond similarly to different halogen substitutions of peptide; -Br substitution at R2-position and -I substitution at R4-position are most effective in improving peptide selectivity for HtrA1-PDZ/HtrA4-PDZ and HtrA2-PDZ/HtrA3-PDZ, respectively; -F substitution would not address substantial effect on peptide selectivity for all the 4 domains. Consequently, the binding affinities of a native peptide ligand DSRIWWV as well as its 4 R2-halogenated counterparts were determined as 1.9, 1.4, 0.5, 0.27, and 0.92 μM, which are basically consistent with computational analysis. This study would help to rationally design selective peptide inhibitors of HtrA family members by using different halogen substitutions.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Peptide selectivity between the PDZ domains of human pregnancy‐related serine proteases (HtrA1, HtrA2, HtrA3, and HtrA4) can be reshaped by different halogen probes

Sun

Wang

2017

J of Molecular Recognition

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“…Later, Liu et al described a rational halogenation strategy to improve biological activity for the peptide ligand, which introduced a geometrically satisfactory halogen bond at the domain-peptide complex interface by systematically optimizing the combination of halogen types and their substitution positions at the indole moiety of peptide Trp-1 residue. 8,9 However, chemical synthesis of non-natural halogenated peptides is technically sophisticated. In addition, the designed halogen bond is vulnerable to its protein environment as this type of noncovalent force is structurally exquisite and highly specific.…”

Section: Introductionmentioning

confidence: 99%

Molecular design of orthogonal stacking system at the complex interface of HtrA PDZ domain with its peptide ligands

Zhang

Pan

et al. 2019

JSCS

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The high temperature requirement A (HtrA) protease plays a crucial role in protein quality control and cell fate. The enzyme contains a catalytic protease domain and a regulatory PDZ domain; the latter determines the substrate specificity of the former by specifically binding to the C-terminal hydrophobic stretch of its partner proteins. Previously, a pentapeptide ligand H3C1 was identified as the potential binder of HtrA PDZ domain using phage display technique. Here, an orthogonal ??cation?? stacking system at the crystal domain?peptide complex interface was analysed by integrating theoretical calculations and experimental assays. It was demonstrated that there is a strong (positive) synergistic effect between the two wings of the stacking system; breaking of cation?? interaction in one wing can largely impair the interaction strength of another wing. The ?-electron contributes primarily to the synergistic effect, although geometric property is also (marginally) responsible for it. Next, the systematic combinations between the four aromatic amino acids (Phe, Tyr, Trp and His) plus one non-aromatic amino acid (Ala) at the two wings of ??cation?? stacking were investigated. It was found that two aromatic substitutions (Phe-4Tyr and Phe-4Trp) at a wing can considerably and moderately improve peptide affinity by 3.2- and 1.5-fold, respectively, whereas the non-aromatic mutations at each wing and at both of them can significantly reduce the affinity with Kd increase from 1.8 (wild type) to 34 ?M and 160 ?M (single-point mutations), as well as 210 ?M (double-point mutation), suggesting that just breaking of one wing can substantially undermine the synergism of orthogonal ??cation?? stacking.

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“…In the structure, the peptide ligand can tightly bind on PDZ surface to compete with HtrA1 substrate for the domain. Previously, we have successfully integrated computational modeling and experimental assay to characterize specific chemical forces in biomolecular system . Here, a geometrically satisfactory halogen bond was rationally designed at the complex interface of HtrA1 PDZ domain with its heptapeptide ligand to promote the domain–peptide binding by combining high‐level ab initio calculations, hybrid quantum mechanics/molecular mechanics (QM/MM) analysis and fluorescence assay.…”

Section: Introductionmentioning

confidence: 99%

Structure‐Based Design of a Br Halogen Bond at the Complex Interface of the Human Placental HtrA1 PDZ Domain with Its Heptapeptide Ligand

Dou

Liu

Cao

et al. 2016

Archiv der Pharmazie

Self Cite

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The shock-induced serine protease HtrA1 is a potential regulator of human placenta development during pregnancy. The protein contains a functional PDZ domain that has been solved in complex with a phage display-derived heptapeptide: Asp-6 Ser-5 Arg-4 Ile-3 Trp-2 Trp-1 Val0 . In this study, a rationally designed halogen bond was introduced to the domain-peptide complex based on its NMR structure in solution. We computationally compared the stabilization energies and hindrance effects due to the presence of different halogens X (X = F, Cl, Br, or I), using a hybrid quantum mechanics/molecular mechanics (QM/MM) approach, and found that the Br atom could considerably promote the peptide binding free energy (ΔΔG = -5.2 kcal/mol). Fluorescence assays confirmed that the peptide affinity to the HtrA1 PDZ domain was improved by approximately sevenfold upon bromination. Structural analysis identified a geometrically perfect halogen bond between the Br atom of the peptide Trp-1 residue and the carbonyl O atom of the HtrA1 Ile385 residue, with a bond length and an interaction energy of d = 3.20 Å and ΔE = -3.7 kcal/mol, respectively.

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Rational Improvement of Peptide Affinity to Human Pregnancy-Related Serine Protease HtrA3 PDZ Domain by Introducing a Halogen Bond to the Domain–Peptide Complex Interface

Cited by 10 publications

References 21 publications

Peptide selectivity between the PDZ domains of human pregnancy‐related serine proteases (HtrA1, HtrA2, HtrA3, and HtrA4) can be reshaped by different halogen probes

Peptide selectivity between the PDZ domains of human pregnancy‐related serine proteases (HtrA1, HtrA2, HtrA3, and HtrA4) can be reshaped by different halogen probes

Molecular design of orthogonal stacking system at the complex interface of HtrA PDZ domain with its peptide ligands

Structure‐Based Design of a Br Halogen Bond at the Complex Interface of the Human Placental HtrA1 PDZ Domain with Its Heptapeptide Ligand

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