Polymer formation by the essential FtsZ protein plays a crucial role in the cytokinesis of most prokaryotes. Lateral associations between these FtsZ polymers to form bundles or sheets are widely predicted to be extremely important for FtsZ function in vivo. We have carried out a study in vitro of FtsZ polymer formation and bundling using linear dichroism (LD) to assess structural properties of the polymers. We demonstrate proof-of-principle experiments to show that LD can be used as a technique to follow FtsZ polymerization, and we present the LD spectra of FtsZ polymers. Our subsequent examination of FtsZ polymer bundling induced by calcium reveals a substantial increase in the LD signal indicative of increased polymer length and rigidity. We also detect a specific conformational change in the guanine moiety associated with bundling, whereas the conformation and configuration of the FtsZ monomers within the polymer remain largely unchanged. We demonstrate that other divalent cations can induce this conformational change in FtsZ-bound GTP coincident with polymer bundling. Therefore, we present "flipping" of the guanine moiety in FtsZ-bound GTP as a mechanism that explains the link between reduced GTPase activity, increased polymer stability, and polymer bundling.
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http://dx.doi.org/10.1074/jbc.M404944200 | DOI Listing |
Nat Commun
January 2025
Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Identifying transitional states is crucial for understanding protein conformational changes that underlie numerous biological processes. Markov state models (MSMs), built from Molecular Dynamics (MD) simulations, capture these dynamics through transitions among metastable conformational states, and have demonstrated success in studying protein conformational changes. However, MSMs face challenges in identifying transition states, as they partition MD conformations into discrete metastable states (or free energy minima), lacking description of transition states located at the free energy barriers.
View Article and Find Full Text PDFNat Commun
January 2025
Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, 518132, China.
Nucleosome is the basic structural unit of the genome. During processes like DNA replication and gene transcription, the conformation of nucleosomes undergoes dynamic changes, including DNA unwrapping and rewrapping, as well as histone disassembly and assembly. However, the wrapping characteristics of nucleosomes across the entire genome, including region-specificity and their correlation with higher-order chromatin organization, remains to be studied.
View Article and Find Full Text PDFChem Asian J
January 2025
University of Shanghai for Science and Technology, School of Materials and Chemistry, Shanghai, CHINA.
Ln-MOFs, composed of lanthanide ions and functional organic ligands, are porous materials with tunable structures and unique luminescent properties. However, the interplay between ligand AIE properties and the framework's "antenna effect" on MOF morphology is understudied. Here, Tb-D-Cam-TPTB was synthesized via solvothermal method using TPTB (persulfurated arene) as the primary ligand, D-Cam as the auxiliary ligand, and Tb3+ as the metal ion.
View Article and Find Full Text PDFTrends Biochem Sci
January 2025
Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, Denmark. Electronic address:
Human glucokinase (GCK) functions as a glucose sensor in the pancreas and liver, where GCK activity regulates insulin secretion and glycogen synthesis, respectively. GCK's low affinity for glucose and the sigmoidal substrate dependency of enzymatic turnover enables it to act as a sensor that makes cells responsive to changes in circulating glucose levels. Its unusual kinetic properties are intrinsically linked to the enzyme's conformational dynamics.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
January 2025
Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX 75080.
The TRAMP complex contains two enzymatic activities essential for RNA processing upstream of the nuclear exosome. Within TRAMP, RNA is 3' polyadenylated by a subcomplex of Trf4/5 and Air1/2 and unwound 3' to 5' by Mtr4, a DExH helicase. The molecular mechanisms of TRAMP assembly and RNA shuffling between the two TRAMP catalytic sites are poorly understood.
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