13 Jun 2023

What Rosalind Franklin truly contributed to the discovery of DNA’s structure (Nature)

Franklin was no victim in how the DNA double helix was solved. An overlooked letter and an unpublished news article, both written in 1953, reveal that she was an equal player. According to journalist Horace Freeland Judson and Franklin’s biographer, Brenda Maddox, Rosalind Franklin has been reduced to the “wronged heroine” of the double helix. She deserves to be remembered not as the victim of the double helix, but as an equal contributor to the solution of the structure.

13 Jun 2023

Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR

Disulfide bond formation is fundamentally important for protein structure and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive its time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfill other favorable contacts.

13 Jun 2023

How did life begin? One key ingredient is coming into view (Nature)

A Nobel-prizewinning scientist’s team has taken a big step forward in its quest to reconstruct an early-Earth RNA capable of building proteins. Ada Yonath, a structural biologist at the Weizmann Institute of Science in Rehovot, Israel, and her team first conceptualized the ‘protoribosome’ idea nearly two decades ago. The lab’s achievements in the past two years — creating a primitive RNA machine that can link two amino acids together— have created a ripple of excitement.

19 Apr 2023

Mapping the conformational landscape of the stimulatory heterotrimeric G protein (Nature Structural & Molecular Biology)

Heterotrimeric G proteins serve as membrane-associated signaling hubs, in concert with their cognate G-protein-coupled receptors. Fluorine nuclear magnetic resonance spectroscopy was employed to monitor the conformational equilibria of the human stimulatory G-protein alpha subunit (G(s)alpha) alone, in the intact G(s)alpha beta(1)gamma(2) heterotrimer or in complex with membrane-embedded human adenosine A(2A) receptor (A(2A)R).The results reveal a concerted equilibrium that is strongly affected by nucleotide and interactions with the beta gamma subunit, the lipid bilayer and A(2A)R. The alpha 1 helix of G(s)alpha exhibits significant intermediate timescale dynamics. The alpha 4 beta 6 loop and alpha 5 helix undergo membrane/receptor interactions and order-disorder transitions respectively, associated with G-protein activation. The alpha N helix adopts a key functional state that serves as an allosteric conduit between the beta gamma subunit and receptor, while a significant fraction of the ensemble remains tethered to the membrane and receptor upon activation.
Fluorine nuclear magnetic resonance spectroscopy of the stimulatory heterotrimeric G protein reveals a conformational landscape shaped by interactions with nucleotides, the lipid bilayer and a G-protein-coupled receptor.

19 Apr 2023

A quantitative map of nuclear pore assembly reveals two distinct mechanisms (Nature)

Understanding how the nuclear pore complex (NPC) is assembled is of fundamental importance to grasp the mechanisms behind its essential function and understand its role during the evolution of eukaryotes(1-4). There are at least two NPC assembly pathways-one during the exit from mitosis and one during nuclear growth in interphase-but we currently lack a quantitative map of these events. Here we use fluorescence correlation spectroscopy calibrated live imaging of endogenously fluorescently tagged nucleoporins to map the changes in the composition and stoichiometry of seven major modules of the human NPC during its assembly in single dividing cells. This systematic quantitative map reveals that the two assembly pathways have distinct molecular mechanisms, in which the order of addition of two large structural components, the central ring complex and nuclear filaments are inverted. The dynamic stoichiometry data was integrated to create a spatiotemporal model of the NPC assembly pathway and predict the structures of postmitotic NPC assembly intermediates.

19 Apr 2023

Structures and mechanisms of tRNA methylation by METTL1–WDR4 (Nature)

Specific, regulated modification of RNAs is important for proper gene expression(1,2). tRNAs are rich with various chemical modifications that affect their stability and function(3,4). 7-Methylguanosine (m(7)G) at tRNA position 46 is a conserved modification that modulates steady-state tRNA levels to affect cell growth(5,6). The METTL1-WDR4 complex generates m(7)G46 in humans, and dysregulation of METTL1-WDR4 has been linked to brain malformation and multiple cancers(7-22). Here we show how METTL1 and WDR4 cooperate to recognize RNA substrates and catalyse methylation. A crystal structure of METTL1-WDR4 and cryo-electron microscopy structures of METTL1-WDR4-tRNA show that the composite protein surface recognizes the tRNA elbow through shape complementarity. The cryo-electron microscopy structures of METTL1-WDR4-tRNA with S-adenosylmethionine or S-adenosylhomocysteine along with METTL1 crystal structures provide additional insights into the catalytic mechanism by revealing the active site in multiple states. The METTL1 N terminus couples cofactor binding with conformational changes in the tRNA, the catalytic loop and the WDR4 C terminus, acting as the switch to activate m(7)G methylation. Thus, our structural models explain how post-translational modifications of the METTL1 N terminus can regulate methylation. Together, our work elucidates the core and regulatory mechanisms underlying m(7)G modification by METTL1, providing the framework to understand its contribution to biology and disease.