It is concluded that the early emergence of the Rossmann fold reflects the chemical and physical constraints of protein folding, explaining both its profound antiquity and sustained longevity.
It is shown that short nucleic acids containing Gquadruplex (G4) structure can also catalyze protein folding and uncovers a previously underappreciated role for nucleic acid in proteostasis and offers a new strategy for studying nucleic acid structure-function relationship at residue level.
A mechanistic model of de novo folding initiation during biosynthesis is infer and a complete atomistic description of a co-translational folding pathway is provided by linking the folding nucleus to downstream partially structured intermediates and the native state is provided.
Ivana V. Bukvin, Julian O. Streit, Tomasz Włodarski et al.· bioRxiv· 0 citations
The results establish ρ analysis as a general framework to probe RNA conformational pathways and function and uncover multiple folding pathways and modulation in pathway flux that are readily understood from the energetic properties of the constituent RNA motifs.
Brant Gracia, Sarah E Nielson, Daniel Herschlag et al.· bioRxiv· 0 citations
Together, these insights position conformational dynamics at the center of understanding and engineering the evolutionary logic of protein function, opening the door to study how proteins are tuned to operate under the nonequilibrium conditions of living cells.
Sixto M. Herrera, Elías Manríquez-Benítez, Exequiel Medina· Current Opinion in Structura...· 0 citations
Dihydroxyacetone kinase (DAK) catalyzes the ATP-dependent phosphorylation of dihydroxyacetone (DHA) and is an important enzyme in artificial starch synthesis. Here, we report the crystal structure of a methylotrophic yeast DAK from Komagataella phaffii (formly Pichia pastoris, PpDAK). ATP was observed at a non-canonical site distinct from the canonical bacterial ATP-binding pocket. Docking further suggested that the canonical pocket remains accessible, indicating flexibility in ATP recognition. Sequence and phylogenetic analyses show that PpDAK clusters within a distinct methylotrophic yeast lineage and that residues surrounding the non-canonical ATP-binding site are conserved among methylotrophic yeasts. In addition, Mg2+ ions were identified in some substrate-binding pockets and docking suggested substantial overlap between Mg2+ and the predicted DHA-binding position. Together, these findings provide structural insights into ATP recognition in fungal DAKs and a framework for future functional studies and enzyme engineering.
Hongli Wei, Yangyang Chen, Fan Zhang et al.· Biochemical and Biophysical...· 0 citations
Ring-like AAA+ (ATPases Associated with diverse cellular Activities) biological machines mediate protein remodeling to assist a broad range of essential cellular functions. The nucleotide-dependent remodeling action involves intra- and inter-ring allosteric communication to generate mechanical force applied onto the substrate by a set of loops that protrude into the central channel. In this study, we probe these allosteric mechanisms through a comparative study of the katanin, a microtubule severing protein including a clade 3 AAA domain, and the double-ring ClpB, a protein disaggregase including both a clade 3 and a clade 5 AAA domain. Our molecular dynamics simulations, combined with machine learning and bioinformatic analysis, reveal both similar mechanisms involving the clade 3 domain and ClpB-specific ones involving communication with the clade 5 domain. We find that both nucleotide and substrate polypeptide binding restrict the conformational landscape sampled by katanin and ClpB, with ligand-specific conformations observed in the latter case. Allosteric contributions of secondary structure elements, ranked by using SHapley Additive exPlanations analysis in machine learning approaches and binary classification of features in ligand states, highlight the important role of regions adjacent to the nucleotide-binding site and the pore loops. Amino acid-level analysis of the allosteric paths reveals that intra-ring cooperativity modulates long-distance communication within the AAA+ protomers.