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Instruments / Technical Area	Publication Details	Published
	Exploring TRF2-dependent DNA distortion through single-DNA manipulation studies Xiaodan Zhao , Vinod Kumar Vogirala , Meihan Liu , Yu Zhou , Daniela Rhodes , Sara Sandin , Jie Yan Communications Biology 7 DOI: 10.1038/s42003-024-05838-x Open Access Show Abstract ▼ Abstract: TRF2 is a component of shelterin, a telomere-specific protein complex that protects the ends of mammalian chromosomes from DNA damage signaling and improper repair. TRF2 functions as a homodimer and its interaction with telomeric DNA has been studied, but its full-length DNA-binding properties are unknown. This study examines TRF2’s interaction with single-DNA strands and focuses on the conformation of the TRF2-DNA complex and TRF2’s preference for DNA chirality. The results show that TRF2-DNA can switch between extended and compact conformations, indicating multiple DNA-binding modes, and TRF2’s binding does not have a strong preference for DNA supercoiling chirality when DNA is under low tension. Instead, TRF2 induces DNA bending under tension. Furthermore, both the N-terminal domain of TRF2 and the Myb domain enhance its affinity for the telomere sequence, highlighting the crucial role of multivalent DNA binding in enhancing its affinity and specificity for telomere sequence. These discoveries offer unique insights into TRF2’s interaction with telomeric DNA.	Feb 2024
I02-Macromolecular Crystallography	Grafting Rhodobacter sphaeroides with red algae Rubisco to accelerate catalysis and plant growth Yu Zhou , Laura H. Gunn , Rosemary Birch , Inger Andersson , Spencer M. Whitney Nature Plants 575 DOI: 10.1038/s41477-023-01436-7 Diamond Proposal Number(s): [11171] Show Abstract ▼ Abstract: Improving the carboxylation properties of Rubisco has primarily arisen from unforeseen amino acid substitutions remote from the catalytic site. The unpredictability has frustrated rational design efforts to enhance plant Rubisco towards the prized growth-enhancing carboxylation properties of red algae Griffithsia monilis GmRubisco. To address this, we determined the crystal structure of GmRubisco to 1.7 Å. Three structurally divergent domains were identified relative to the red-type bacterial Rhodobacter sphaeroides RsRubisco that, unlike GmRubisco, are expressed in Escherichia coli and plants. Kinetic comparison of 11 RsRubisco chimaeras revealed that incorporating C329A and A332V substitutions from GmRubisco Loop 6 (corresponding to plant residues 328 and 331) into RsRubisco increased the carboxylation rate (kcatc) by 60%, the carboxylation efficiency in air by 22% and the CO2/O2 specificity (Sc/o) by 7%. Plastome transformation of this RsRubisco Loop 6 mutant into tobacco enhanced photosynthesis and growth up to twofold over tobacco producing wild-type RsRubisco. Our findings demonstrate the utility of RsRubisco for the identification and in planta testing of amino acid grafts from algal Rubisco that can enhance the enzyme’s carboxylase potential.	Jun 2023
Krios I-Titan Krios I at Diamond	The structural basis of translational control by eIF2 phosphorylation Tomas Adomavicius , Margherita Guaita , Yu Zhou , Martin D. Jennings , Zakia Latif , Alan Roseman , Graham D. Pavitt Nature Communications 10, 2136 DOI: 10.1038/s41467-019-10167-3 Diamond Proposal Number(s): [15436, 16619] Open Access Show Abstract ▼ Abstract: Protein synthesis in eukaryotes is controlled by signals and stresses via a common pathway, called the integrated stress response (ISR). Phosphorylation of the translation initiation factor eIF2 alpha at a conserved serine residue mediates translational control at the ISR core. To provide insight into the mechanism of translational control we have determined the structures of eIF2 both in phosphorylated and unphosphorylated forms bound with its nucleotide exchange factor eIF2B by electron cryomicroscopy. The structures reveal that eIF2 undergoes large rearrangements to promote binding of eIF2α to the regulatory core of eIF2B comprised of the eIF2B alpha, beta and delta subunits. Only minor differences are observed between eIF2 and eIF2αP binding to eIF2B, suggesting that the higher affinity of eIF2αP for eIF2B drives translational control. We present a model for controlled nucleotide exchange and initiator tRNA binding to the eIF2/eIF2B complex.	May 2019

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