NMR structural and dynamical characterization of a two-step walk through peptide sequence space is presented; from the (cid:2) N peptide sequence, which functions to activate transcription antitermination, to a peptide sequence that inhibits antitermination.
ApexFold, an environment-conditioned AI framework that combines sequence representations with physicochemical descriptors of the surrounding medium to predict circular-dichroism-derived fractions of α-helical, β-like, and unstructured conformations is developed.
M. D. Torres, Hanqun Cao, César de la Fuente-Núñez· bioRxiv· 0 citations
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.
Koh Seya, Tatsuya Corlett, Hamza Giaffar et al.· bioRxiv· 0 citations
Class III aminotransferases represent a structurally and functionally unique subgroup. However, the contribution of specific loop elements to their active-site architecture and cofactor-dependent structural transitions remain underexplored. We elucidated the structural framework underlying the catalytic function of class III fold Pyridoxal 5′-phosphate-dependent aminotransferase from the Antarctic bacterium Hymenobacter sp. PAMC 26554 (HyAT), and report its crystal structure at 2.31 Å resolution. The structure revealed a canonical class III fold organized as a functional homotetramer. Structural analysis identified a proline-containing motif (P-x-P) within the α10-α11 loop, which induces intrinsic disorder at the active-site entrance in the apo-form and revealed that a cooperative disorder-to-order transition is requisite for active-site assembly upon cofactor binding. We propose that this flexible loop region may be involved in modulating substrate access. Notably, this proline motif was conserved in homologs from Hyperthermophiles, despite the cold-adapted nature of HyAT. This convergence implies a common evolutionary strategy where the geometric constraints of proline are exploited to decouple local active-site dynamics from global scaffold stability, thereby addressing the stability–activity trade-off across diverse thermal environments. Our findings provide new molecular insights into the structural dynamics of class III aminotransferases and highlight evolutionary strategies for tuning enzyme flexibility in extreme environments.
Jisub Hwang, Hackwon Do, Jun Hyuck Lee· Crystals· 0 citations
This method enables rapid and accurate identification of structural repeats by calculating the distance between Cα atoms in the peptide backbone by calculating the distance between Cα atoms in the peptide backbone.
Gurleen Kaur, Madhumathi Sanjeevi, Srimaha Gandhi et al.· Journal of Applied Crystallo...· 0 citations
Together, these results show that designed repeat-protein folding is governed by seed formation, interface propagation, and terminal boundary conditions, and establish intramolecular crosslinking as a strategy for rationally reshaping folding landscapes in designed proteins.
Melanie Weiß, Anna Lisa Heit, L. Milles et al.· bioRxiv· 0 citations
This work reviews the computational and experimental approaches that disentangle folding and function at scale, revealing a dark energy component and providing new insights into how biological information flows from sequence to structure to function and back to sequence.
Ezequiel A. Galpern, Federico Caamaño, Ignacio E. Sánchez et al.· 0 citations
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