An allosteric signaling pathway of human 3-phosphoglycerate kinase from force distribution analysis.
3-Phosphogycerate kinase (PGK) is a two domain enzyme, which transfers a phosphate group between its two substrates, 1,3-bisphosphoglycerate bound to the N-domain and ADP bound to the C-domain. Indispensable for the phosphoryl transfer reaction is a large conformational change from an inactive open to an active closed conformation via a hinge motion that should bring substrates into close proximity. The allosteric pathway resulting in the active closed conformation has only been partially uncovered. Using Molecular Dynamics simulations combined with Force Distribution Analysis (FDA), we describe an allosteric pathway, which connects the substrate binding sites to the interdomain hinge region. Glu192 of alpha-helix 7 and Gly394 of loop L14 act as hinge points, at which these two secondary structure elements straighten, thereby moving the substrate-binding domains towards each other. The long-range allosteric pathway regulating hPGK catalytic activity, which is partially validated and can be further tested by mutagenesis, highlights the virtue of monitoring internal forces to reveal signal propagation, even if only minor conformational distortions, such as helix bending, initiate the large functional rearrangement of the macromolecule.
Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
Zoltan
Z
Palmai
Molecular Biomechanics, Heidelberger Institut für Theoretische Studien gGmbH, Heidelberg, Germany.
Christian
C
Seifert
Molecular Biomechanics, Heidelberger Institut für Theoretische Studien gGmbH, Heidelberg, Germany ; MPG-CAS Partner Institute and Key Laboratory for Computational Biology, Shanghai, China.
Frauke
F
Gräter
Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
Erika
E
Balog
D000465:Algorithms; D000495:Allosteric Site; D001665:Binding Sites; D004252:DNA Mutational Analysis; D006801:Humans; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D016296:Mutagenesis; D010735:Phosphoglycerate Kinase / Q000235:genetics / Q000378:metabolism*; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D015398:Signal Transduction; D013314:Stress, Mechanical
C577282:PGK1 protein, human; D010735:Phosphoglycerate Kinase