Enzymes in a human cytoplasm model organize into submetabolon complexes

• 成果类型: Article
• 署名作者: Russell, Premila P. Samuel; Rickard, Meredith M.; Pogorelov, Taras V.; Gruebele, Martin
• 署名单位: University of Illinois System; University of Illinois Urbana-Champaign; Washington University (WUSTL); Saint Louis University; University of Illinois System; University of Illinois Urbana-Champaign; University of Illinois System; University of Illinois Urbana-Champaign; University of Illinois System; University of Illinois Urbana-Champaign; University of Illinois System; University of Illinois Urbana-Champaign; University of Illinois System; University of Illinois Urbana-Champaign; University of Illinois System; University of Illinois Urbana-Champaign
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-13175
• DOI: 10.1073/pnas.2414206122
• 发表日期: 2025-02-04
• 关键词: red-blood-cell; glyceraldehyde-3-phosphate dehydrogenase; quinary structure; phosphoglycerate kinase; glycolytic-enzymes; protein; simulations; metabolon; diffusion; DYNAMICS

摘要

Enzyme-enzyme interactions are fundamental to the function of cells. Their atomistic mechanisms remain elusive mainly due to limitations of in- cell measurements. We address this challenge by atomistically modeling, for a total of approximate to 80 mu s, a slice of the human cell cytoplasm that includes three successive enzymes along the glycolytic path(PGK), and phosphoglycerate mutase (PGM). We tested the model for nonspecific protein stickiness, an artifact of current atomistic force fields in crowded environments. The simulations reveal that the human enzymes co- organize in- cell into transient submetabolon complexes, consistent with previous experimental results. Our data both reiterate known specificity between GAPDH and PGK and reveal extensive direct interactions between GAPDH and PGM. Our simulations further reveal, through force field benchmarking, the critical role of protein solvation in facilitating these enzyme-enzyme interactions. Transient interenzyme interactions with mu s lifetime occur repeatedly in our simulations via specific sticky protein surface patches, with interactions often mediated by charged patch residues. Some of the residues that interact frequently with one another lie in or near the active site of the enzymes. We show that some of these patches correspond to a general mode to interact with several partners for promiscuous enzymes like GAPDH. We further show that the non- native yeast PGK is stickier than human PGK in our human cytoplasm model, supporting the idea of evolutionary pressure to reduce sticking. Our cytoplasm modeling paves the way toward capturing the atomistic dynamics of an entire enzymatic pathway in- cell.