Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size

Area of Science:

• Biochemistry
• Computational Biology
• Structural Biology

Background:

• Human hemoglobin (Hb) exists in two quaternary states: T (tense) and R (relaxed).
• Previous molecular dynamics (MD) simulations of Hb's T-state produced results inconsistent with experimental data, showing an unexpected transition to an R-like state.
• The stability of the T-state is crucial for understanding hemoglobin's allosteric regulation.

Purpose of the Study:

• To investigate the stability of the unliganded human hemoglobin (Hb) T-state using molecular dynamics simulations.
• To identify the conditions necessary for accurately simulating the T-state stability and validate the Perutz model.
• To assess the impact of solvent box size and protonation states on simulation outcomes.

Main Methods:

• Utilized molecular dynamics (MD) simulations to model human hemoglobin (Hb).
• Employed standard and significantly larger periodic solvent boxes (ten times the standard size) to assess the role of the hydrophobic effect.
• Investigated the influence of histidine-146 (His146) protonation on T-state stability.

Main Results:

• The unliganded Hb T-state is stable only in significantly larger solvent boxes, approximately ten times the standard size.
• This large solvent box size is necessary to accurately represent the hydrophobic effect, which stabilizes the T-state.
• T-state stability in large boxes is contingent upon the protonation of His146, supporting the Perutz model at an atomistic level.

Conclusions:

• Accurate simulation of human hemoglobin's T-state requires substantially larger solvent boxes than conventionally used.
• The hydrophobic effect, crucial for T-state stabilization, is adequately modeled only in these larger simulation environments.
• Protonation of His146 is essential for T-state stability, providing atomistic evidence for the Perutz model and highlighting the need for careful consideration of simulation parameters in future studies.