Molecular Dynamics Study of Amyloidogenic Mutants of Human Lysozyme

Uliana Tarabara ,Valeriya Trusova ,Kateryna Vus ,Olga Ryzhova ,Galyna Gorbenko

doi:10.26565/2312-4334-2018-4-04

Uliana Tarabara , Valeriya Trusova + Show 3 more

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https://doi.org/10.26565/2312-4334-2018-4-04

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Abstract

The mutants of human lysozyme are capable of fibril formation implicated in the etiology of familial systemic or renal amyloidosis. A series of 100 ns thermal unfolding molecular dynamics (MD) simulations with WT human lysozyme and its seven amyloidogenic variants (I56T, D67H, F57I, W64R, Y54N, F57I/T70N and T70N/W112R) have been performed at 500 K. The molecular dynamics simulations were performed with GROMACS software (version 5.1) using the CHARMM36m force field. The MD results have been analysed in terms of the parameters characterizing both the global and local protein structure, such as the backbone root mean-square deviation, gyration radius, solvent accessible surface area, the root mean-square fluctuations and the secondary structure content. Depending on the observed effects, the examined variants of human lysozyme have been roughly divided into three groups comprising of mutants with faster (Y54N and F57I/T70N), similar (D67H and I56T) or slower (W64, F57I and T70N/W112R) unfolding rate compared to the wild-type counterpart. The analysis of the protein fluctuational behavior revealed that in most mutants the β-domain displays stronger fluctuations (except the W64R and F57I) and higher flexibility of the C- and D-helices relative to the native lysozyme with the exception of W64R and Y54N which show marked decrease (W64R) or increase (Y54N) in mobility of almost all residues. The analysis of secondary structure evolution provided evidence for higher stability of α-domain compared to β-domain. The results obtained reinforce the idea that mutation-induced global structural destabilization is not the only factor contributing to protein misfolding, the modifications in conformation and dynamics of selected protein regions may also play significant role in amyloid fibril formation.

Highlights

The mutants of human lysozyme are capable of fibril formation implicated in the etiology of familial systemic or renal amyloidosis
The thermal unfolding trajectories of WT lysozyme and its mutants were analysed in terms of the parameters reflecting the changes in both the global and local protein structure, root mean-square deviations (RMSD), radius of gyration (Rg), solvent-accessible surface area (SASA), root mean-square fluctuations of the C-alpha atoms (RMSF) and the secondary structure content
Previous unfolding simulations showed that D67H and I56T have larger RMSD values compared to WT [33,34]

Summary

Introduction

The mutants of human lysozyme are capable of fibril formation implicated in the etiology of familial systemic or renal amyloidosis. Анализ флуктуационного поведения белка показал, что у большинства мутантов β-домену присущи более сильные флуктуации (за исключением W64R и F57I) и большая гибкость C- и D-спиралей по сравнению с нативным лизоцимом, за исключением W64R и Y54N, у которых выявлено заметное снижение (W64R) или увеличение (Y54N) подвижности почти всех остатков. A variety of factors controlling the mechanisms and kinetics of amyloid formation have been identified and subdivided into two main groups The former involves extrinsic factors, such as environmental conditions (pH, temperature, pressure, ionic strength, extent of molecular crowding, concentration of denaturing agents or reactive oxygen species, etc.), molecular chaperone and ubiquitin-proteasome cellular systems; while the latter implicates intrinsic factors, associated with fundamental features of polypeptide chain (net charge, mean hydrophobicity, secondary structure propensities, etc.) [7,8]. Fibrillization-favoring conditions are created by lowering pH, elevating temperature, adding organic solvents or denaturants, etc., while in vivo, abnormal partial unfolding or folding may arise from mutations, oxidative or heat stress or destabilization of protein structure upon adsorption at interfaces formed by cell membranes [9,10,11,12]

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