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Structural Investigation of sickle cell hemoglobin and deoxy- human hemoglobin beta 6 Glu -> Trp using molecular
dynamics simulation
Hadi Abroshan, Gholamabbas Parsafar*
Department of Chemistry, Sharif University of Technology, Tehran, Iran Laboratory of Theoretical Physical Chemistry
[email protected] , [email protected]
Abstract:
Molecular dynamics simulation of sickle cell hemoglobin (HbS) in deoxy form and deoxy-human hemoglobin beta 6 Glu -> Trp were performed Using NAMD and VMD programs and results were used for comparing structure stability during temperature increase from 50 to 350 K by evaluating the root mean-square deviation for each amino acid from its equilibrium position at 310 K. In addition, by using the calculated solvent accessible surface, we have evaluated and compared the molecular surface with temperature increase. By focusing on the results for deoxy-human hemoglobin beta 6 Glu -> Trp, the reasons of specific stereochemistry which decrease polymerization of the mention molecule (in contrast with HbS) are presented.
Key words: Molecular dynamics simulation, Hemoglobin S, Structural stability
Introduction
Human hemoglobin A (Hb A) is generally designated as a2Aþ2A. Alpha chains usually form tetramer with other hemoglobin chains which they are more stable than those tetramers form with the þ chain. The human a chain consist of 141 amino acids in a linear sequence. The heme group in this chain is bonded covalently by a linkage between the heme iron and the imidazole of a histidine residue at the position 87. The þ chain (146 residues) is slightly longer than a chain. Heme binds at the þ His 92. Sickle cell ammonia is result of a mutation at the 6th amino acid of beta chains in hemoglobin (HB) molecule.
During this mutation the negative charge wild amino acid (Glu) is replaced by the neutral hydrophobic amino acid (Val) and formed a new type of
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Hemoglobin called sickle cell Hemoglobin (HBS). The deoxy form of the sickle Hb aggregates to form long and rigid rods that deform the erythrocytes into their characteristic sickle shape (Edelstein, 1981; Padlan & love, 1985; Rodgers et al. , 1987;
Carragher et al. , 1988).
Method
For the initial structure of HbS we have chosen the X-ray structure (PDB code: 2Hbs).
For the initial structure of deoxy-human hemoglobin beta 6 Glu -> Trp, we have chosen the X-ray structure (PDB code: 6HBW). Like an ordinary X-ray structure, this crystal structure has no hydrogen atoms. So we have added the hydrogens. All of the His20, 45, 50, and 72 of the alpha1 and alpha2 subunits and His77 and 117 of beta1 and beta2 subunits were modeled as positively charged residues. All Glu and Asp residues were modeled as negatively charged because of the charges of their neighboring residues. The whole system had the total charge of 8.0. Entire molecule was covered in a sphere of radius 40 Å. We have added NaCl as the counter ions with concentration of
0.1 M. So 1 Na+ and 9 Cl- ions, added to make the whole system chargeless. Whole system comprised of 23695 atoms. We have used the Charmm force field (par_all27_prot_lipid_na.inp) and NAMD program version2.6, with MD simulation for the entire system. The time step of MD simulation was 2 fs and the cutoff radius of 12 Å.
All bonds involving hydrogen are considered to be rigid. The MD simulation was performed at 350, 300, 250, 200, 150, 100, and 50 K with 40000, 40000, 45000, 50000, 55000, 60000 and 65000 steps. To analyze the solvent accessible surface for equilibrated structures the molmol program with 1 Å for solvent radius and 5 for precision was used.
Results
Solvent accessible surface was calculated for the structures at end of the equilibrium the plot of the results shows that two molecules are not so different from surface point of view, see figure 1. Such a result is reasonable since the difference between two molecules is in one amino acid residue only.
By evaluating the root mean-square deviation for each amino acid from equilibrated structure at 310 K, we could distinguish the most change area of two molecules. For
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example figure 2 shows the root mean-square deviations (RMSD) for all amino acids at the beta chain of 2Hbs.
In addition, with focusing on 6HBW at different temperatures we have founded that hydrogen bonds play an important role in the stable stereochemistry of the mention molecule which reduces the polymerization.
Figure1. Solvent accessible surface versus temperatures.
Figure 2. RMSD for all amino acids at the beta chain of the 2Hbs
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