Molecular Dynamics of Hemoglobin Reveals Structural Alterations and Explains the Interactions Driving Sickle Cell Fibrillation

Abstract

In sickle cell anemia, deoxyhemoglobin deforms RBCs by forming fibrils inside that disintegrate on oxygenation. We studied 100 ns long all-atom molecular dynamics (MD) for sickle and normal hemoglobin fibril models to understand this process, complemented by multiple 1 μs MD for a single tetramer of sickle and normal hemoglobin in deoxy and oxy states. We find that the presence of hydrophobic residues without a bulky side chain at β-6 in hemoglobin is the reason for the stability of the fibrils. Moreover, the free energy landscapes from MD of hemoglobin starting in the tensed (T) state capture the putative transition from T to relaxed (R) state, associated with oxygen binding. The three conformational wells in the landscapes are characterized by the quaternary changes where one αβ dimer rotates with respect to the other. The conformational changes from the oxygenation of sickle hemoglobin hinder the intermolecular contacts necessary for fibril formation.

Protein Aggregation-Inhibition: A Therapeutic Route from Parkinson's Disease to Sickle Cell Anemia

“…MD simulations of sickle and normal hemoglobin and hemoglobin fibril models were also recently reported [134][135][136] . Maity and Pal 135 argued that the presence of hydrophobic residues without a bulky side chain at β6 in hemoglobin explained the stability of the fibrils, consistent with the experiments by Adachi et al 137 , which showed that some substituents in the 6 position, such as phenylalanine and tryptophan, polymerized less readily compared to deoxy-HbS and that when oversaturated polymerization occurred without the delay time observed for HbS. Adachi et al argued that the difficulty of insertion of the bulky side chains of phenylalanine and tryptophan into the hydrophobic acceptor pocket on an adjacent tetramer could inhibit nuclei formation prior to polymerization.…”

Searching for Structure: Characterizing the Protein Conformational Landscape with Clustering-Based Algorithms

“…By plotting the cluster centers or representatives resulting from each method on the corresponding FEL, we can compare the degree to which a method captures the conformational space. It is important to note that we do not apply clustering to the FEL as done in other studies. , The evaluation of how well a clustering method performs is based on how well the resulting cluster centers cover the FEL minima and the states around and between minima, without populating the entire space, i.e., while still differentiating between the input conformations.…”

“…29 A single-point mutation (E6V) in the β chains of hemoglobin leads to sickle cell anemia. 30,31 This mutation causes the aggregation of hemoglobin fibrils in the absence of O 2 (T) that leads to the deformation of red blood cells; however, when O 2 is present (R), the fibrils disintegrate. 31,32 Having a means of characterizing the conformational landscape is crucial for identifying states for these more heterogeneous proteins/regions, which are essential for understanding enzymatic mechanisms or the effects of allosteric modulators and of disease-related mutations.…”

“…It is important to note that we do not apply clustering to the FEL as done in other studies. 31,73 The evaluation of how well a clustering method performs is based on how well the resulting cluster centers cover the FEL minima and the states around and between minima, without populating the entire space, i.e., while still differentiating between the input conformations.…”

“…MD simulations were also used to identify a nucleotide-dependent conformational transition in secondary structure from a loop in the G-actin filament to a helix in the F-actin filament. − Another classic example of extensive ligand-induced allosteric control over a quaternary protein structure is hemoglobin . A single-point mutation (E6V) in the β chains of hemoglobin leads to sickle cell anemia. , This mutation causes the aggregation of hemoglobin fibrils in the absence of O 2 (T) that leads to the deformation of red blood cells; however, when O 2 is present (R), the fibrils disintegrate. , Having a means of characterizing the conformational landscape is crucial for identifying states for these more heterogeneous proteins/regions, which are essential for understanding enzymatic mechanisms or the effects of allosteric modulators and of disease-related mutations.…”