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Plant Polypeptide Hormone Systemin Prefers Polyproline II Conformation in Solution.

ABSTRACT: Systemin, an 18 amino-acid-signaling peptide, was the first plant polypeptide hormone to be discovered. Earlier structural studies involving NMR spectroscopy indicated a lack of definite structure in solution while circular dichroism spectroscopy suggested the presence of left-handed polyproline II (PPII) conformation. Here, we report the results of molecular dynamics simulations of the peptide in explicit solvent with two different force fields, namely, ff99SBildn and ff99IDPs, both of which showed a large propensity for PPII-like conformations in spite of showing differing features for other conformational characteristics. More remarkably, the conformations with predicted chemical shifts that agreed better with the NMR observations had a larger than average PPII content, especially for the ff99IDPs force field. An independent docking calculation of the molecule with the putative receptor SR160 also retained this conformational preference for PPII structure. The results suggest PPII to be an important class of conformation for systemin which may have a role in its bioactivity.

SUBMITTER: Dutta Chowdhury S

PROVIDER: S-EPMC6644842 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature

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Plant Polypeptide Hormone Systemin Prefers Polyproline II Conformation in Solution.

Dutta Chowdhury Saikat S Lahiri Ansuman A

ACS omega 20171017 10

Systemin, an 18 amino-acid-signaling peptide, was the first plant polypeptide hormone to be discovered. Earlier structural studies involving NMR spectroscopy indicated a lack of definite structure in solution while circular dichroism spectroscopy suggested the presence of left-handed polyproline II (PPII) conformation. Here, we report the results of molecular dynamics simulations of the peptide in explicit solvent with two different force fields, namely, ff99SBildn and ff99IDPs, both of which sh ...[more]

PMID: 31457269

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Project description:BACKGROUND: Secondary structures are elements of great importance in structural biology, biochemistry and bioinformatics. They are broadly composed of two repetitive structures namely ?-helices and ?-sheets, apart from turns, and the rest is associated to coil. These repetitive secondary structures have specific and conserved biophysical and geometric properties. PolyProline II (PPII) helix is yet another interesting repetitive structure which is less frequent and not usually associated with stabilizing interactions. Recent studies have shown that PPII frequency is higher than expected, and they could have an important role in protein-protein interactions. METHODOLOGY/PRINCIPAL FINDINGS: A major factor that limits the study of PPII is that its assignment cannot be carried out with the most commonly used secondary structure assignment methods (SSAMs). The purpose of this work is to propose a PPII assignment methodology that can be defined in the frame of DSSP secondary structure assignment. Considering the ambiguity in PPII assignments by different methods, a consensus assignment strategy was utilized. To define the most consensual rule of PPII assignment, three SSAMs that can assign PPII, were compared and analyzed. The assignment rule was defined to have a maximum coverage of all assignments made by these SSAMs. Not many constraints were added to the assignment and only PPII helices of at least 2 residues length are defined. CONCLUSIONS/SIGNIFICANCE: The simple rules designed in this study for characterizing PPII conformation, lead to the assignment of 5% of all amino as PPII. Sequence-structure relationships associated with PPII, defined by the different SSAMs, underline few striking differences. A specific study of amino acid preferences in their N and C-cap regions was carried out as their solvent accessibility and contact patterns. Thus the assignment of PPII can be coupled with DSSP and thus opens a simple way for further analysis in this field.

Dataset Information

Plant Polypeptide Hormone Systemin Prefers Polyproline II Conformation in Solution.

Publications

Plant Polypeptide Hormone Systemin Prefers Polyproline II Conformation in Solution.

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