Natural supramolecular protein assemblies

Supramolecular protein assemblies are an emerging area within the chemical sciences, which combine the topological structures of the field of supramolecular chemistry and the state-of-the-art chemical biology approaches to unravel the formation and function of protein assemblies. Recent chemical and biological studies on natural multimeric protein structures, including fibers, rings, tubes, catenanes, knots, and cages, have shown that the quaternary structures of proteins are a prerequisite for their highly specific biological functions. In this review, we illustrate that a striking structural diversity of protein assemblies is present in nature. Furthermore, we describe structure–function relationship studies for selected classes of protein architectures, and we highlight the techniques that enable the characterisation of supramolecular protein structures

Mechanism of biomolecular recognition of trimethyllysine by the fluorinated aromatic cage of KDM5A PHD3 finger

The understanding of biomolecular recognition of posttranslationally modified histone proteins is centrally important to the histone code hypothesis. Despite extensive binding and structural studies on the readout of histones, the molecular language by which posttranslational modifications on histone proteins are read remains poorly understood. Here we report physical-organic chemistry studies on the recognition of the positively charged trimethyllysine by the electron-rich aromatic cage containing PHD3 finger of KDM5A. The aromatic character of two tryptophan residues that solely constitute the aromatic cage of KDM5A was fine-tuned by the incorporation of fluorine substituents. Our thermodynamic analyses reveal that the wild-type and fluorinated KDM5A PHD3 fingers associate equally well with trimethyllysine. This work demonstrates that the biomolecular recognition of trimethyllysine by fluorinated aromatic cages is associated with weaker cation-π interactions that are compensated by the energetically more favourable trimethyllysine-mediated release of high-energy water molecules that occupy the aromatic cage

Minimal information for studies of extracellular vesicles 2018 (MISEV2018):a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines

The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles (“MISEV”) guidelines for the field in 2014. We now update these “MISEV2014” guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points

Thermodynamic analyses of Sgf29-H3K4me2 and Sgf29-H3K4me3 interactions.

<p>Representative ITC experiments showing the titration of H3K4me3 (top row, A-D) and H3K4me2 (bottom row, E-H) peptides to Sgf29 (first column, A,E), D266E (second column B, F), D266N (third column, C, G) and D266Y (fourth column, D, F).</p

CD spectra of various expressions of wild-type Sgf29 its D266 variants, and the Y238F and Y245F variants.

<p>CD experiments were carried out at the concentration of 0.1 mg ml^-1 in 10 mM sodium phosphate buffer (pH 7.5).</p

Tm values for Sgf29 and its variants as determined by DSF.^[a]

<p>^[a] Tm as measured by DSF ± SD (Measured in triplicate)</p><p>Tm values for Sgf29 and its variants as determined by DSF.<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139205#t001fn001" target="_blank">^[a]</a></p

Tm curves of A) wild-type Sgf29 and its D266 variants and B) Sgf29 and its Y238 and Y245 variants.^[a]

<p>Tm curves of A) wild-type Sgf29 and its D266 variants and B) Sgf29 and its Y238 and Y245 variants.^[a]</p

Representative ITC experiments displaying binding of H3K4me3 and H3K4me2 to Y238F and Y245F Sgf29 variants.

<p>A) H3K4me3-Y238F, B) H3K4me3-Y245F, C) H3K4me2-Y238F and D) H3K4me2-Y245F.</p

ITC experiments showing binding of A) ARTKme3QTAGKS and B) ARTKme3QTA to WT Sgf29.

<p>Thermodynamics of binding for A) <i>K</i>_d = 4.0 ± 0.6 μM, Δ<i>G</i>° = - 7.4 ± 0.1 kcal mol^-1, Δ<i>H</i>° = - 8.0 ± 0.1 kcal mol^-1,-TΔ<i>S</i>° = 0.6 ± 0.1 kcal mol^-1 and for B) <i>K</i>_d = 9.0 ± 0.5 μM, Δ<i>G</i>° = - 6.9 ± 0.1 kcal mol^-1, Δ<i>H</i>° = - 7.8 ± 0.1 kcal mol^-1,-TΔ<i>S</i>° = 0.9 ± 0.1 kcal mol^-1.</p