First observation of metal ion-induced structural fluctuations of α-helical peptides by using diffracted X-ray tracking

Diffracted X-ray Tracking for Observing the Internal Motions of Individual Protein Molecules and Its Extended Methodologies

In 1998, the diffracted X-ray tracking (DXT) method pioneered the attainment of molecular dynamics measurements within individual molecules. This breakthrough revolutionized the field by enabling unprecedented insights into the complex workings of molecular systems. Similar to the single-molecule fluorescence labeling technique used in the visible range, DXT uses a labeling method and a pink beam to closely track the diffraction pattern emitted from the labeled gold nanocrystals. Moreover, by utilizing X-rays with extremely short wavelengths, DXT has achieved unparalleled accuracy and sensitivity, exceeding initial expectations. As a result, this remarkable advance has facilitated the search for internal dynamics within many protein molecules. DXT has recently achieved remarkable success in elucidating the internal dynamics of membrane proteins in living cell membranes. This breakthrough has not only expanded our knowledge of these important biomolecules but also has immense potential to advance our understanding of cellular processes in their native environment.

Analysis of the Structural Dynamics of Proteins in the Ligand-Unbound and -Bound States by Diffracted X-ray Tracking

Although many protein structures have been determined at atomic resolution, the majority of them are static and represent only the most stable or averaged structures in solution. When a protein binds to its ligand, it usually undergoes fluctuation and changes its conformation. One attractive method for obtaining an accurate view of proteins in solution, which is required for applications such as the rational design of proteins and structure-based drug design, is diffracted X-ray tracking (DXT). DXT can detect the protein structural dynamics on a timeline via gold nanocrystals attached to the protein. Here, the structure dynamics of single-chain Fv antibodies, helix bundle-forming de novo designed proteins, and DNA-binding proteins in both ligand-unbound and ligand-bound states were analyzed using the DXT method. The resultant mean square angular displacements (MSD) curves in both the tilting and twisting directions clearly demonstrated that structural fluctuations were suppressed upon ligand binding, and the binding energies determined using the angular diffusion coefficients from the MSD agreed well with the binding thermodynamics determined using isothermal titration calorimetry. In addition, the size of gold nanocrystals is discussed, which is one of the technical concerns of DXT.

Conformational changes of α-helical peptides with different hydrophobic residues induced by metal-ion binding

We designed peptides that formed helix bundle structures upon binding of the metal-ions to His residues to form a stable hydrophobic core, in order to analyze the effects of Ala, Val, Ile, and Leu residues, located in the hydrophobic core, together with His, on the conformational changes in respective peptides designated as HA, HV, HI, and HL, respectively. Circular dichroism measurements showed that HV and HI changed from random coil to helix bundle structures upon Zn2+ binding, similar to that observed for HA, while HL existed in the helix bundle structure even in the absence of Zn2+. Electron spin resonance measurements showed that Cu2+ coordination of HI and HL was quite different from that of HA and HV, indicating that HA and HV fluctuated to a greater extent in the solution, despite that their apparent α-helical contents being similar to those of HI and HL. This was also supported by the results obtained from the analyses of thermal stabilities. The change in the structural fluctuation for each peptide upon Zn2+ binding was evaluated based on binding thermodynamics using isothermal titration calorimetry. The structural flexibility in the metal-ion-bound state was found to be in the order HA > HV > HI, and that in the metal-ion-unbound state was found to be greater for HI than that for HL.

Structural dynamics of a DNA-binding protein analyzed using diffracted X-ray tracking

Diffracted X-ray tracking (DXT) is one of methods for the real-time evaluation of protein structural dynamics by detecting the movement of a gold-nanocrystal attached to a target protein. However, one of the technical concerns is the size of the gold-nanocrystals, which are larger than the protein. In our previous results of mean square angular displacement curves in DXT analysis, dynamical movements of the DNA-binding protein, c-Myb R2R3, were observed in only one population in either DNA-unbound or -bound state, and was found to decrease upon DNA binding. In this study, c-Myb R2R3 dynamical movements were re-evaluated with a low density of the protein immobilized on the DXT substrate, to decrease the possibility that the gold-nanocrystals attached to more than one R2R3 molecule. We observed two dynamical moving populations in the DNA-bound state, which could be classified due to electrostatic attraction and repulsion between the DNA-protein complexes, and determined the apparent angular diffusion constant, which was similar to the value calculated in our previous study. We showed more real movement of the protein could be observed by lowering the immobilization density of the protein.