Probing the local conformational flexibility in receptor recognition: mechanistic insight from an atomic-scale investigation

Abstract

Inherent protein conformational flexibility is important for biomolecular recognition, but this critical property is often neglected in several studies. This event can lead to large deviations in the research results. In the current contribution, we disclose the effects of the local conformational flexibility on receptor recognition by using an atomic-scale computational method. The results indicated that both static and dynamic reaction modes have noticeable differences, and these originated from the structural features of the protein molecules. Dynamic interaction results displayed that the structural stability and conformational flexibility of the proteins had a significant influence on the recognition processes. This point related closely to the characteristics of the flexible loop regions where bixin located within the protein structures. The energy decomposition analyses and circular dichroism results validated the rationality of the recognition studies. More importantly, the conformational and energy changes of some residues around the bixin binding domain were found to be vital to biological reactions. These microscopic findings clarified the nature of the phenomenon that the local conformational flexibility could intervene in receptor recognition. Obviously, this report may provide biophysical evidence for the exploration of the structure-function relationships of the biological receptors in the human body.

Fig. 1. Molecular docking of bixin docked to HSA (panel (A) and panel (B)) and AGP (panel (C) and panel (D)). HSA and AGP showed in surface colored in orange and yellow, respectively, and the ball-and-stick model displays bixin, colored as per the atoms and possess meshy surface of electron spin density. The key amino acid residues around bixin have been described in stick model, green and salmon stick model indicates hydrogen bonds and hydrophobic effects between the proteins and bixin, respectively; and blue stick model explains π–π conjugated effects between the Tyr-27, Phe-49, Phe-112 residues and bixin (panel (D)). (For clarification of the references to color in this figure legend, the reader is referred to the web version of the article).

Fig. 2. Hydrophobic effects between the amino acid residues comprising the binding domains on HSA (panel (A)) and AGP (panel (B)) and the bixin. The polypeptide chain of HSA and AGP implied in surface colored in orange and yellow, respectively, and the ball-and-stick model suggests bixin, colored as per the atoms. The multi-colored ribbon on the left-hand side of the graph hints the strength of hydrophobicity and the brown signifies strong hydrophobicity while the blue symbolizes forceful hydrophilicity. (For illumination of the references to color in this figure legend, the reader is referred to the web version of the article).

Fig. 3. Calculated Root-Mean-Square Deviation (RMSD) for the initial X-ray crystal structures for the backbone C_α atoms of HSA (panel (A)) and AGP (panel (C)), and the bixin and the backbone C_α atoms of HSA (panel (B)) and AGP (panel (D)) from MD simulation at a temperature of 300 K with respect to their docking results as a function of the simulation time. The blue and red trajectories illustrate RMSD data for the backbone C_α atoms of proteins and the bixin, respectively.

Fig. 4. Superimposition of the average conformations of MD simulation on the original conformations of molecular docking resulting from the HSA–bixin (panel (A), panel (B) and panel (C)) and the AGP–bixin (panel (D), panel (E) and panel (F)) adducts. HSA and AGP revealed in surface colored in orange and yellow (initial) and both pink (average), respectively, and the original and average conformations of bixin divulged in cyan and pink ball-and-stick model, respectively. The critical amino acid residues around bixin have been portrayed in stick model, orange and yellow stick model depicts initial conformations of the residues in HSA and AGP, respectively, whereas dark pink stick model represents average conformations of the residues in both proteins. (For explication of the references to color in this figure legend, the reader is referred to the web version of the article).

Fig. 5. Root-Mean-Square Fluctuation (RMSF) of the backbone of each residue atomic positions for the unbound (olive (panel (A)) and orange (panel (B))) and bound (red (panel (A)) and blue (panel (B))) HSA (panel (A)) and AGP (panel (B)) as a function of the atom location along the polypeptide chain, respectively.

Fig. 6. The decompositions of free energy of recognition per-residue for the proteins–bixin biosystems. The amino acid residues contributing predominantly to the HSA–bixin (panel (A)) and the AGP–bixin (panel (B)) bioconjugations are underlined by wine or blue dash dotted line, respectively.