PH-Induced Changes in Polypeptide Conformation: Force-Field Comparison with Experimental Validation.

Maria Sammalkorpi,Piotr Batys,Piotr Bonarek,Maria Morga

doi:10.1021/acs.jpcb.0c01475

Abstract

Microsecond-long all-atom molecular dynamics (MD) simulations, circular dichroism, laser Doppler velocimetry, and dynamic light-scattering techniques have been used to investigate pH-induced changes in the secondary structure, charge, and conformation of poly l-lysine (PLL) and poly l-glutamic acid (PGA). The employed combination of the experimental methods reveals for both PLL and PGA a narrow pH range at which they are charged enough to form stable colloidal suspensions, maintaining their α-helix content above 60%; an elevated charge state of the peptides required for colloidal stability promotes the peptide solvation as a random coil. To obtain a more microscopic view on the conformations and to verify the modeling performance, peptide secondary structure and conformations rising in MD simulations are also examined using three different force fields, i.e., OPLS-AA, CHARMM27, and AMBER99SB*-ILDNP. Ramachandran plots reveal that in the examined setup the α-helix content is systematically overestimated in CHARMM27, while OPLS-AA overestimates the β-sheet fraction at lower ionization degrees. At high ionization degrees, the OPLS-AA force-field-predicted secondary structure fractions match the experimentally measured distribution most closely. However, the pH-induced changes in PLL and PGA secondary structure are reasonably captured only by the AMBER99SB*-ILDNP force field, with the exception of the fully charged PGA in which the α-helix content is overestimated. The comparison to simulations results shows that the examined force fields involve significant deviations in their predictions for charged homopolypeptides. The detailed mapping of secondary structure dependency on pH for the polypeptides, especially finding the stable colloidal α-helical regime for both examined peptides, has significant potential for practical applications of the charged homopolypeptides. The findings raise attention especially to the pH fine tuning as an underappreciated control factor in surface modification and self-assembly.

Highlights

L-lysine (PLL), and poly L-glutamic acid (PGA) often serve as a model pair of pH-tunable polypeptides (PPs)
A summary of the bulk physicochemical characteristics of poly L-lysine (PLL) and PGA molecules measured in the laser Doppler velocimetry (LDV) and dynamic light scattering (DLS) measurements is gathered in Figure 2 presents the pH dependence of the electrophoretic mobility μ as a function of pH as measured by the LDV
The ability to accurately reproduce pH-induced changes in PLL and PGA homopolypeptide secondary structure and conformation by different atomistic resolution molecular modeling force fields was investigated via the molecular dynamics (MD) method

Summary

Introduction

L-lysine (PLL), and poly L-glutamic acid (PGA) often serve as a model pair of pH-tunable polypeptides (PPs). Due to the wide range of applications, extensive research to understand the pH-induced changes of the PLL and PGA structure by a variety of experimental methods including turbidimetry, dynamic light-scattering, and zeta-potential analysis exists.[8] The peptide conformational changes have been investigated using circular dichroism (CD),[9−13] UV resonance Raman spectroscopy,[14,15] Fourier-transform infrared spectroscopy,[11] and low-angle laser light measurements.[10] It should be mentioned that besides the pH, the structure and conformation of PPs can be controlled by the ionic strength,[16] temperature,[17] or their chirality.[18] The existing works show that both PGA and PLL change their secondary structure from random coil to α-helix when the pH shifts from neutral to lower (for PGA) or higher (for PLL). Even though the pH dependency has received significant attention, studies connecting directly the peptide protonation state and secondary structure remain lacking

Methods

Results

Conclusion