Solvent accessibility of E1α and E1β residues with known missense mutations causing pyruvate dehydrogenase complex (PDC) deficiency: Impact on PDC‐E1 structure and function

Abstract

Pyruvate dehydrogenase complex deficiency is a major cause of primary lactic acidemia resulting in high morbidity and mortality, with limited therapeutic options. PDHA1 mutations are responsible for >82% of cases. The E1 component of PDC is a symmetric dimer of heterodimers (αβ/α′β′) encoded by PDHA1 and PDHB. We measured solvent accessibility surface area (SASA), utilized nearest‐neighbor analysis, incorporated sequence changes using mutagenesis tool in PyMOL, and performed molecular modeling with SWISS‐MODEL, to investigate the impact of residues with disease‐causing missense variants (DMVs) on E1 structure and function. We reviewed 166 and 13 genetically resolved cases due to PDHA1 and PDHB, respectively, from variant databases. We expanded on 102 E1α and 13 E1β nonduplicate DMVs. DMVs of E1α Arg112‐Arg224 stretch (exons 5‐7) and of E1α Arg residues constituted 40% and 39% of cases, respectively, with invariant Arg349 accounting for 22% of arginine replacements. SASA analysis showed that 86% and 84% of residues with nonduplicate DMVs of E1α and E1β, respectively, are solvent inaccessible (“buried”). Furthermore, 30% of E1α buried residues with DMVs are deleterious through perturbation of subunit‐subunit interface contact (SSIC), with 73% located in the Arg112‐Arg224 stretch. E1α Arg349 represented 74% of buried E1α Arg residues involved in SSIC. Structural perturbations resulting from residue replacements in some matched neighboring pairs of amino acids on different subunits involved in SSIC at 2.9‐4.0 Å interatomic distance apart, exhibit similar clinical phenotype. Collectively, this work provides insight for future target‐based advanced molecular modeling studies, with implications for development of novel therapeutics for specific recurrent DMVs of E1α.

Simulations of Pathogenic E1α Variants: Allostery and Impact on Pyruvate Dehydrogenase Complex-E1 Structure and Function

“…Clustering analysis of E1 variant with R349H replacements on both the α and α’ subunits (Supplementary Figure S16B) showed that the most populated clusters were conformationally similar to the state X (open α-Loop A and closed α’-Loop A) of E1 variant with R349C replacements on both the α and α’ subunits (Figure 4B). Interestingly, similar average reduction in cultured fibroblast-based PDC activity in males affected with PDCD is observed with R349C (21.5% control mean activity, min/max 8/40, STD 13.6, n=5) 30,59 and R349H (21.2% control mean activity, min/max 10/50, STD 11.7, n=11) 30,59 . These results in conjunction with similar average reductions in PDC activity (for R349C and R349H replacements in male) indicate that Loop A may not only be important for anchoring the ligand (and hence the enzymatic catalysis), but may also be important for substrate intake and/or acetyl transfer to the E2.…”

“…These results show that the type of amino acid replacement at a specific E1α region could have different E1 dynamic consequences at Loop A, which is consistent with the clinical variability noted in females with different replacements of specific E1α amino acids. 30,59…”

“…30,59 Females with R349H and R349C replacements also have severe neonatal/infantile phenotype as males with fibroblast-based PDC activity ranging from 15-45% control mean (n=3). 30 The communication network involving α-Helix 3 on the β and β’ subunits is most likely correlated with the flip-flop action that coordinates the active sites. Hence, any alteration to the communication provided by this region can affect the flip-flop action.…”

“…17,39,41 This residue is also in close proximity to E1α H63, Y89, and R90, all of which interact with the phosphate groups of TPP. 16,30,39 Second, Loop A residues are in close proximity to regions important for the coordination of Mg +2 .…”

“…30 DMMs of two buried residues in E1α, R349 and W185, destabilize SSICs and result in low PDC activity with clear clinical impact, but the mechanism by which this perturbation is affecting function is not yet clear. 30 PDC activity is mainly regulated via the phosphorylation of the E1 component with regulation independent of phosphorylation also reported. 11,[31][32][33][34] Inactivation of the E1 component of human PDC is achieved via phosphorylation of E1α S203, S264, and S271 located on loops formed by E1α amino acid stretches R259-R282 (Loop A, highly conserved) and N195-E205 (Loop B, highly conserved) (Figure 1).…”