bims-lances 2024-05-12 papers

Issue of 2024‒05‒12
four papers selected by
James M. Krieger, National Centre for Biotechnology

Curr Opin Struct Biol. 2024 May 08. pii: S0959-440X(24)00052-6. [Epub ahead of print]86 102825

Single-particle Cryo-EM and molecular dynamics simulations: A perfect match.

Lars V Bock, Maxim Igaev, Helmut Grubmüller.

Knowledge of the structure and dynamics of biomolecules is key to understanding the mechanisms underlying their biological functions. Single-particle cryo-electron microscopy (cryo-EM) is a powerful structural biology technique to characterize complex biomolecular systems. Here, we review recent advances of how Molecular Dynamics (MD) simulations are being used to increase and enhance the information extracted from cryo-EM experiments. We will particularly focus on the physics underlying these experiments, how MD facilitates structure refinement, in particular for heterogeneous and non-isotropic resolution, and how thermodynamic and kinetic information can be extracted from cryo-EM data.

DOI: https://doi.org/10.1016/j.sbi.2024.102825

J Struct Biol. 2024 May 07. pii: S1047-8477(24)00035-2. [Epub ahead of print] 108095

Structure and conformational variability of the HER2-trastuzumab-pertuzumab complex.

Rémi Ruedas, Rémi Vuillemot, Thibault Tubiana, Jean-Marie Winter, Laura Pieri, Ana-Andreea Arteni, Camille Samson, Slavica Jonic, Magali Mathieu, Stéphane Bressanelli.

Single particle analysis from cryogenic transmission electron microscopy (cryo-EM) is particularly attractive for complexes for which structure prediction remains intractable, such as antibody-antigen complexes. Here we obtain the detailed structure of a particularly difficult complex between human epidermal growth factor receptor 2 (HER2) and the antigen-binding fragments from two distinct therapeutic antibodies binding to distant parts of the flexible HER2, pertuzumab and trastuzumab (HTP). We highlight the strengths and limitations of current data processing software in dealing with various kinds of heterogeneities, particularly continuous conformational heterogeneity, and in describing the motions that can be extracted from our dataset. Our HTP structure provides a more detailed view than the one previously available for this ternary complex. This allowed us to pinpoint a previously overlooked loop in domain IV that may be involved both in binding of trastuzumab and in HER2 dimerization. This finding may contribute to explain the synergistic anticancer effect of the two antibodies. We further propose that the flexibility of the HTP complex, beyond the difficulties it causes for cryo-EM analysis, actually reflects regulation of HER2 signaling and its inhibition by therapeutic antibodies. Notably we obtain our best data with ultra-thin continuous carbon grids, showing that with current cameras their use to alleviate particle misdistribution is compatible with a protein complex of only 162 kDa. Perhaps most importantly, we provide here a dataset for such a smallish protein complex for further development of software accounting for continuous conformational heterogeneity in cryo-EM images.

Keywords: Antibody-antigen complex; Continuous conformational variability; Cryogenic electron microscopy; HER2 signaling

DOI: https://doi.org/10.1016/j.jsb.2024.108095

Nat Commun. 2024 May 06. 15(1): 3775

Platform-directed allostery and quaternary structure dynamics of SAMHD1 catalysis.

Oliver J Acton, Devon Sheppard, Simone Kunzelmann, Sarah J Caswell, Andrea Nans, Ailidh J O Burgess, Geoff Kelly, Elizabeth R Morris, Peter B Rosenthal, Ian A Taylor.

SAMHD1 regulates cellular nucleotide homeostasis, controlling dNTP levels by catalysing their hydrolysis into 2'-deoxynucleosides and triphosphate. In differentiated CD4+ macrophage and resting T-cells SAMHD1 activity results in the inhibition of HIV-1 infection through a dNTP blockade. In cancer, SAMHD1 desensitizes cells to nucleoside-analogue chemotherapies. Here we employ time-resolved cryogenic-EM imaging and single-particle analysis to visualise assembly, allostery and catalysis by this multi-subunit enzyme. Our observations reveal how dynamic conformational changes in the SAMHD1 quaternary structure drive the catalytic cycle. We capture five states at high-resolution in a live catalytic reaction, revealing how allosteric activators support assembly of a stable SAMHD1 tetrameric core and how catalysis is driven by the opening and closing of active sites through pairwise coupling of active sites and order-disorder transitions in regulatory domains. This direct visualisation of enzyme catalysis dynamics within an allostery-stabilised platform sets a precedent for mechanistic studies into the regulation of multi-subunit enzymes.

DOI: https://doi.org/10.1038/s41467-024-48237-w

Methods Mol Biol. 2024 ;2799 269-280

Modeling and Simulation of the NMDA Receptor at Coarse-Grained and Atomistic Levels.

Wenjun Zheng, Xing Liu.

N-Methyl-D-aspartate (NMDA) receptors are glutamate-gated excitatory channels that play essential roles in brain functions. While high-resolution structures were solved for an allosterically inhibited form of functional NMDA receptor, other key functional states (particularly the active open-channel state) have not yet been resolved at atomic resolutions. To decrypt the molecular mechanism of the NMDA receptor activation, structural modeling and simulation are instrumental in providing detailed information about the dynamics and energetics of the receptor in various functional states. In this chapter, we describe coarse-grained modeling of the NMDA receptor using an elastic network model and related modeling/analysis tools (e.g., normal mode analysis, flexibility and hotspot analysis, cryo-EM flexible fitting, and transition pathway modeling) based on available structures. Additionally, we show how to build an atomistic model of the active-state receptor with targeted molecular dynamics (MD) simulation and explore its energetics and dynamics with conventional MD simulation. Taken together, these modeling and simulation can offer rich structural and dynamic information which will guide experimental studies of the activation of this key receptor.

Keywords: Coarse-grained modeling; Cryo-EM flexible fitting; Elastic network model; Hotspot residues; Molecular dynamics; NMDA receptor; Normal mode analysis; Transition pathway modeling

DOI: https://doi.org/10.1007/978-1-0716-3830-9_15