Alpha-helical Protein Structures Research Articles

Comparative analysis of nanomechanics of protein filaments under lateral loading

Using a combination of explicit solvent atomistic simulation and continuum theory, here we study the lateral deformation mechanics of three distinct protein structures: an amyloid fibril, a beta helix, and an alpha helix. We find that the two β-sheet rich structures - amyloid fibril and beta helix, with persistence lengths on the order of μm - are well described by continuum mechanical theory, but differ in the degree to which shear deformation affects the overall bending behavior. The alpha helical protein structure, however, with a persistence length on the order of one nanometer, does not conform to the continuum theory and its deformation is dominated by entropic elasticity due to significant fluctuations. This study provides fundamental insight into the nanomechanics of widely found protein motifs and insight into molecular-scale deformation mechanisms, as well as quantitative estimates of Young's modulus and shear modulus in agreement with experimental results.

Solid State NMR Observation of the Geometry of Kinked Protein Helices

Oriented sample solid state nuclear magnetic resonance (ssNMR) is a technique for characterizing the structure of membrane proteins in a nearly native environment. 15N anisotropic chemical shift and 15N-1H dipolar couplings in two dimensional separated local field ssNMR spectra provide precise restraints on the orientation of peptide planes with respect to the membrane normal in alpha helical protein structures. These restraints can be utilized in structure determination and provide a straightforward technique for characterization of helical orientation using PISA wheel analysis.

Fourier transform infrared microspectroscopy detects changes in protein secondary structure associated with desiccation tolerance in developing maize embryos

Isolated immature maize (Zea mays L.) embryos have been shown to acquire tolerance to rapid drying between 22 and 25 d after pollination (DAP) and to slow drying from 18 DAP onward. To investigate adaptations in protein profile in association with the acquisition of desiccation tolerance in isolated, immature maize embryos, we applied in situ Fourier transform infrared microspectroscopy. In fresh, viable, 20- and 25-DAP embryo axes, the shapes of the different amide-I bands were identical, and this was maintained after flash drying. On rapid drying, the 20-DAP axes had a reduced relative proportion of alpha-helical protein structure and lost viability. Rapidly dried 25-DAP embryos germinated (74%) and had a protein profile similar to the fresh control axes. On slow drying, the alpha-helical contribution in both the 20- and 25-DAP embryo axes increased compared with that in the fresh control axes, and survival of desiccation was high. The protein profile in dry, mature axes resembled that after slow drying of the immature axes. Rapid drying resulted in an almost complete loss of membrane integrity in the 20-DAP embryo axes and much less so in the 25-DAP axes. After slow drying, low plasma membrane permeability ensued in both the 20- and 25-DAP axes. We conclude that slow drying of excised, immature embryos leads to an increased proportion of alpha-helical protein structures in their axes, which coincides with additional tolerance of desiccation stress.

Soliton excitations in alpha-helical protein structures

We propose a general theory for soliton excitations in alpha-helical protein structures. In this framework, the interaction between peptide groups is separated into the Amide I exciton-phonon coupling effect and the effect of anharmonicity of phonon. In most of previous theories, only one of the two effects has been taken into account. Expressions for both effects are taken so that they coincide with the previous theoretical results in limiting cases. In the general case we show that both effects should be taken into account.

Dynamical Structure of Alpha Helical Proteins

AbstractVibrational structures of a vibron soliton are studied in terms of the classical vibron model of the α‐helical protein molecule. It is shown that the dynamical structures of the α‐helical protein molecule are described by three types of internal oscillations of vibron solitons which are governed by a set of coupled nonlinear Schrödinger equations.