title: Molecular dynamics analysis of the structural and dynamic properties of the functionally enhanced hepta-variant of mouse 5-aminolevulinate synthase.
abstract: Heme biosynthesis, a complex, multistage, and tightly controlled process, starts with 5-aminolevulinate (ALA) production, which, in metazoa and certain bacteria, is a reaction catalyzed by 5-aminolevulinate synthase (ALAS), a pyridoxal 5'-phosphate (PLP)-dependent enzyme. Functional aberrations in ALAS are associated with several human diseases. ALAS can adopt open and closed conformations, with segmental rearrangements of a C-terminal, 16-amino acid loop and an α-helix regulating accessibility to the ALAS active site. Of the murine erythroid ALAS (mALAS2) forms previously engineered to assess the role of the flexible C-terminal loop versus mALAS2 function one stood out due to its impressive gain in catalytic power. To elucidate how the simultaneously introduced seven mutations of this activity-enhanced variant affected structural and dynamic properties of mALAS2, we conducted extensive molecular dynamics simulation analysis of the dimeric forms of wild-type mALAS2, hepta-variant and Rhodobacter capsulatus ALAS (aka R. capsulatus HemA). This analysis revealed that the seven simultaneous mutations in the C-terminal loop, which extends over the active site of the enzyme, caused the bacterial and murine proteins to adopt different conformations. Specifically, a new β-strand in the mutated 'loop' led to interaction with two preexisting β-strands and formation of an anti-parallel three-stranded β-sheet, which likely endowed the murine hepta-variant a more 'stable' open conformation than that of wild-type mALAS2, consistent with a kinetic mechanism involving a faster closed-to-open conformation transition and product release for the mutated than wild-type enzyme. Further, the dynamic behavior of the mALAS2 protomers was strikingly different in the two dimeric forms.
authors.affiliation: a Department of Molecular Medicine , Morsani College of Medicine, University of South Florida , Tampa , FL 33612 , USA.
authors.forename: Insung
authors.initials: I
authors.lastname: Na
authors.affiliation: a Department of Molecular Medicine , Morsani College of Medicine, University of South Florida , Tampa , FL 33612 , USA.
authors.forename: Shelly
authors.initials: S
authors.lastname: DeForte
authors.affiliation: a Department of Molecular Medicine , Morsani College of Medicine, University of South Florida , Tampa , FL 33612 , USA.
authors.forename: Bosko M
authors.initials: BM
authors.lastname: Stojanovski
authors.affiliation: a Department of Molecular Medicine , Morsani College of Medicine, University of South Florida , Tampa , FL 33612 , USA.|b Department of Chemistry , College of Arts and Sciences, University of South Florida , Tampa , FL 33612 , USA.
authors.forename: Gloria C
authors.initials: GC
authors.lastname: Ferreira
authors.affiliation: a Department of Molecular Medicine , Morsani College of Medicine, University of South Florida , Tampa , FL 33612 , USA.|c USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine , University of South Florida , Tampa , Florida 33612 , USA.|d Laboratory of Structural Dynamics, Stability and Folding of Proteins , Institute of Cytology, Russian Academy of Sciences , St. Petersburg , Russia.
authors.forename: Vladimir N
authors.initials: VN
authors.lastname: Uversky
mesh_terms: D000624:5-Aminolevulinate Synthetase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D000595:Amino Acid Sequence; D000818:Animals; D055162:Biocatalysis; D020134:Catalytic Domain; D006801:Humans; D007700:Kinetics; D051379:Mice; D056004:Molecular Dynamics Simulation; D009154:Mutation; D011487:Protein Conformation; D016354:Rhodobacter capsulatus / Q000201:enzymology / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity
chemical_list: D000624:5-Aminolevulinate Synthetase
keywords: 5-aminolevulinate synthase; active site loop; molecular dynamic