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The protozoan parasite Trichomonas vaginalis contains two nearly identical triosephosphate isomerases (TvTIMs) that dissociate into stable monomers and dimerize upon substrate binding. Herein, we compare the role of the "ball and socket" and loop 3 interactions in substrate assisted dimer assembly in both TvTIMs. We found that point mutants at the "ball" are only 39 and 29-fold less catalytically active than their corresponding wild-type counterparts, whereas Δloop 3 deletions are 1502 and 9400-fold less active. Point and deletion mutants dissociate into stable monomers. However, point mutants assemble as catalytic competent dimers upon binding of the transition state substrate analog PGH, whereas loop 3 deletions remain monomeric. A comparison between crystal structures of point and loop 3 deletion monomeric mutants illustrates that the catalytic residues in point mutants and wild-type TvTIMs are maintained in the same orientation, whereas the catalytic residues in deletion mutants show an increase in thermal mobility and present structural disorder that may hamper their catalytic role. The high enzymatic activity present in monomeric point mutants correlates with the formation of dimeric TvTIMs upon substrate binding. In contrast, the low activity and lack of dimer assembly in deletion mutants suggests a role of loop 3 in promoting the formation of the active site as well as dimer assembly. Our results suggest that in TvTIMs the active site is assembled during dimerization and that the integrity of loop 3 and ball and socket residues is crucial to stabilize the dimer.
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http://dx.doi.org/10.1016/j.bbapap.2017.07.014 | DOI Listing |
Proc Natl Acad Sci U S A
September 2025
Martin A. Fisher School of Physics, Brandeis University, Waltham, MA 02453.
Programmable self-assembly has recently enabled the creation of complex structures through precise control of the interparticle interactions and the particle geometries. Targeting ever more structurally complex, dynamic, and functional assemblies necessitates going beyond the design of the structure itself, to the measurement and control of the local flexibility of the intersubunit connections and its impact on the collective mechanics of the entire assembly. In this study, we demonstrate a method to infer the mechanical properties of multisubunit assemblies using cryogenic electron microscopy (cryo-EM) and RELION's multi-body refinement.
View Article and Find Full Text PDFJ Chem Phys
September 2025
August Chełkowski Institute of Physics, University of Silesia in Katowice, 75 Pułku Piechoty 1, 41-500 Chorzów, Poland.
In this paper, we investigated the thermal, dynamical, and structural properties, as well as association patterns, in 3-phenyl-1-propanol (3P1Pol) and 3-phenyl-1-propanal (3P1Pal), with special attention paid to the latter compound. Both systems turned out to be good glass formers, differing by 17 K in the glass transition temperature, which indicated a strong change in the self-assembly pattern. This supposition was further confirmed by the analysis of dielectric spectra, where, apart from the α-relaxation, also a unique Debye (D)-mode, being a fingerprint of the self-association, characterized by different dynamical properties (dielectric strength, timescale separation from the α-process), was detected in both samples.
View Article and Find Full Text PDFChem Sci
August 2025
Dipartimento di Scienze Chimiche, Università degli studi di Padova via Marzolo 1 35131 Padova Italy
While photoisomerization has dominated the design of photoswitchable catalysts, this work introduces an alternative approach: leveraging light-induced photodimerization to assemble catalytically active species. The adopted strategy is based on a acrylamidylpyrene derivative equipped with a TACN·Zn(ii) catalytic unit. This system undergoes a visible-light-induced [2 + 2] cycloaddition, which is both regioselective and reversible, to form a catalytically active photodimer.
View Article and Find Full Text PDFJ Biol Chem
September 2025
Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, 16802; Center for Structural Biology, Penn State University, University Park, PA 16802; Center for RNA Molecular Biology, Penn State University, University Park, PA 16802. Electronic address:
Despite the overall conservation of ribosomes across all domains of life, differences in their 3D architecture, rRNA sequences, ribosomal protein composition, and translation factor requirements reflect lineage-specific adaptations to environmental niches. In the domain Archaea, structural studies have primarily focused on non-methanogenic thermophiles and halophiles, leaving it unclear whether these represent the broader archaeal domain. Here, we report the cryo-electron microscopy (cryo-EM) structure of the ribosome from Methanosarcina acetivorans, a previously unreported high-resolution structure from a model mesophilic methanogenic archaeon.
View Article and Find Full Text PDFEur J Cell Biol
August 2025
Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Wendlingweg 2, Aachen 52074, Germany. Electronic address:
Keratins are the largest and most diverse group of intermediate filament proteins, providing structural integrity and mechanical strength to epithelial cells. Although their assembly as heterodimers is well established, the specific pairing preferences and molecular basis of keratin dimerisation remain largely unknown. Here, we employ a high-throughput computational pipeline that integrates AlphaFold Multimer (AFM) modelling, VoroIF-GNN interaction interface quality assessment, interaction energy calculations and structural comparisons with experimentally solved structures to systematically investigate keratin heterodimerisation and to provide a guideline for further analysis of intermediate filament assembly.
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