bims-lances 2025-02-23 papers

Nature. 2025 Feb 20.

Structural dynamics of human fatty acid synthase in the condensing cycle.

Wooyoung Choi, Chengmin Li, Yifei Chen, Yongqiang Wang, Yifan Cheng.

Long chain fatty acids are the building blocks of fat in human bodies. In mammals, fatty acid synthase (FASN) contains multiple enzymatic domains to catalyze all chemical reactions needed for de novo fatty acid synthesis1. While the chemical reactions carried out by these enzymatic domains are well defined, how the dimeric FASN with an open architecture continuously catalyzes such reactions to synthesize a complete fatty acid remains elusive. Here, using a strategy of tagging and purifying endogenous FASN in HEK293 for single particle cryogenic electron microscopy studies, we characterized the structural dynamics of endogenous human FASN. We captured the conformational snapshots of various functional substates in the condensing cycle and developed a procedure to analyze particle distribution landscape of FASN with different orientations between its condensing and modifying wings. Together, we reveal that FASN function does not require large rotational motion between its two major functional domains during the condensing cycle, and that the catalytic reactions in condensing cycle carried out by two monomers are unsynchronized. Our data thus provide a new composite view of FASN dynamics during the fatty acid synthesis condensing cycle.

DOI: https://doi.org/10.1038/s41586-025-08782-w

Curr Opin Struct Biol. 2025 Feb 13. pii: S0959-440X(25)00010-7. [Epub ahead of print]91 102992

Combining cryo-electron microscopy (cryo-EM) with orthogonal solution state methods to define the molecular basis of the phosphoprotein phosphatase family regulation and substrate specificity.

Wolfgang Peti, Sathish K R Padi, Rebecca Page.

Protein phosphatases are dynamic enzymes that exhibit complex regulatory mechanisms, with disruptions in these regulatory processes associated with disease. It is now clear that many phosphatases assemble into large macromolecular complexes via the interaction of phosphatase-specific regulatory proteins and substrates containing short linear motifs (SLiMs) or short helical motifs (SHelMs). Here, we review how cryo-electron microscopy (cryo-EM) integrated with orthogonal methods to study dynamic protein-protein interactions (NMR spectroscopy, hydrogen-deuterium exchange mass spectrometry, among others) is leading to new discoveries about the mechanisms controlling phosphatase assembly, substrate recruitment and dephosphorylation and, in turn, are providing novel strategies for targeting phosphatase-related diseases. This review focuses on the recently determined structures and regulation of the phosphoprotein phosphatase (PPP) family of ser/thr phosphatases-PP1, PP2A, Calcineurin and PP5.

DOI: https://doi.org/10.1016/j.sbi.2025.102992

Protein Sci. 2025 Mar;34(3): e70038

Conformational flexibility associated with remote residues regulates the kinetic properties of glutamate dehydrogenase.

Barsa Kanchan Jyotshna Godsora, Parijat Das, Prasoon Kumar Mishra, Anjali Sairaman, Sandip Kaledhonkar, Narayan S Punekar, Prasenjit Bhaumik.

Glutamate dehydrogenase (GDH) is a pivotal metabolic enzyme in all living organisms, and some of the GDHs exhibit substrate-dependent homotropic cooperativity. However, the mode of allosteric communication during the homotropic effect in GDHs remains poorly understood. In this study, we examined two homologous GDHs, Aspergillus niger GDH (AnGDH) and Aspergillus terreus GDH (AtGDH), with differing substrate utilization kinetics to uncover the factors driving their distinct behavior. We report the crystal structures and first-ever cryo-EM structures of apo- AtGDH and AnGDH that captured arrays of conformational ensembles. A wider mouth opening (~ 21 Å) is observed for the cooperative AnGDH as compared to the non-cooperative AtGDH (~17 Å) in their apo states. A network of interactions related to the substitutions in Domain II influence structural flexibility in these GDHs. Remarkably, we have identified a distant substitution (R246 to S) in Domain II, as a part of this network, which can impact the mouth opening and converts non-cooperative AtGDH into a cooperative enzyme. Our study demonstrates that remote residues can influence structural and kinetic properties in homologous GDHs.

Keywords: allostery; cryo‐EM; crystal structure; glutamate dehydrogenase; homotropic cooperativity; intrinsic domain dynamics; kinetic properties; remote residue substitution

DOI: https://doi.org/10.1002/pro.70038