Structural Cues for Understanding eEF1A2 Moonlighting

Spontaneous mutations in the EEF1A2 gene cause epilepsy and severe neurological disabilities in children. The crystal structure of eEF1A2 protein purified from rabbit skeletal muscle reveals a post-translationally modified dimer that provides information about the sites of interaction with numerous binding partners, including itself, and maps these mutations onto the dimer and tetramer interfaces. The spatial locations of the side chain carboxylates of Glu301 and Glu374, to which phosphatidylethanolamine is uniquely attached via an amide bond, define the anchoring points of eEF1A2 to cellular membranes and interorganellar membrane contact sites. Additional bioinformatic and molecular modeling results provide novel structural insight into the demonstrated binding of eEF1A2 to SH3 domains, the common MAPK docking groove, filamentous actin, and phosphatidylinositol-4 kinase IIIβ. In this new light, the role of eEF1A2 as an ancient, multifaceted, and articulated G protein at the crossroads of autophagy, oncogenesis and viral replication appears very distant from the “canonical” one of delivering aminoacyl-tRNAs to the ribosome that has dominated the scene and much of the thinking for many decades.     

电子显微学在结构生物学研究中的新进展

电子显微学是结构生物学的重要分支，已经成为一种公认的研究生物大分子、超分子复合体及亚细胞结构的有力手段。本文先回顾了近期电子显微学在技术上的新进展，后概述了生物电子显微学的三个组成部分——电子晶体学，单颗粒技术，电子断层成像术的基本原理，技术方法与研究现状。最后，对电子显微学与其他结构生物学研究手段的结合以及电子显微学的未来发展做了简单的展望。     

定量电子晶体学硼对Ni3Al的电荷密度分布的影响

阐述了定量电子晶体学测定晶体电荷密度分布的基本原理和方法，不足之处和改善途径。以硼对Ｎｉ３Ａｌ的电荷密度分布的影响为实例，介绍了定量电子晶体学在研究晶体电子结构方面的应用前景。     

PGRP-LB: An Inside View into the Mechanism of the Amidase Reaction

Peptidoglycan recognition proteins (PGRPs) are ubiquitous among animals and play pivotal functions in insect immunity. Non-catalytic PGRPs are involved in the activation of immune pathways by binding to the peptidoglycan (PGN), whereas amidase PGRPs are capable of cleaving the PGN into non-immunogenic compounds. Drosophila PGRP-LB belongs to the amidase PGRPs and downregulates the immune deficiency (IMD) pathway by cleaving meso-2,6-diaminopimelic (meso-DAP or DAP)-type PGN. While the recognition process is well analyzed for the non-catalytic PGRPs, little is known about the enzymatic mechanism for the amidase PGRPs, despite their essential function in immune homeostasis. Here, we analyzed the specific activity of different isoforms of Drosophila PGRP-LB towards various PGN substrates to understand their specificity and role in Drosophila immunity. We show that these isoforms have similar activity towards the different compounds. To analyze the mechanism of the amidase activity, we performed site directed mutagenesis and solved the X-ray structures of wild-type Drosophila PGRP-LB and its mutants, with one of these structures presenting a protein complexed with the tracheal cytotoxin (TCT), a muropeptide derived from the PGN. Only the Y78F mutation abolished the PGN cleavage while other mutations reduced the activity solely. Together, our findings suggest the dynamic role of the residue Y78 in the amidase mechanism by nucleophilic attack through a water molecule to the carbonyl group of the amide function destabilized by Zn²⁺.     

High-Resolution Electron Microscopy Observations of Stacking Faults in β-SiC

Structural images of the stacking faults in β-SiC were obtained with a high-resolution electron microscope. Stacking faults initially present in β-SiC powder particles were eliminated as grain growth proceeded at elevated temperatures.     

热浸镀铝钢扩散层的AlFe3C0.5相

采用740℃热浸镀铝方法,在20碳钢表面制备热浸镀铝层。镀铝层经850℃扩散处理4 h后,采用SEM和XRD确定扩散层的相组成,采用TEM研究组成相的晶体学取向关系。分析AlFe3C0.5相的形成原因。结果表明：扩散层与基体之间存在Fe3Al、FeAl和点阵常数为0.377 nm的针叶状AlFe3C0.5相;针状AlFe3C0.5与Fe3Al相之间存在的晶体学取向关系是（220）Fe3Al//（1^-11）AlFe 3C0.5、[11^-0]Fe3Al//[1^-23^-]AlFe 3 C0.5。     

Towards ETEM serial crystallography: Electron diffraction from liquid jets

A sufficiently thin column of liquid was produced to permit penetration with a 200 keV electron beam as evidenced by the observation of diffraction rings due to the intermolecular spacing of the liquid samples. For liquid thickness below 800 nm, the diffraction rings became visible above the inelastic background. Studies were carried out in the environmental chamber of a transmission electron microscope using water and isopropanol.     

An introduction to computational crystallography:the relationship between aluminum-based spinel structures and their morphologies

Computing technology is developing very fast and has permeated among many fields of sci-ence and technology, giving rise to many interdisciplinary subjects. Crystallography, originating from the activity of mining and smelting, has now become a comprehensive subject concerning crystal growth mechanism, chemical composition, structural morphology and physical properties and its research scope is widened by introducing many new achievements from basic sciences such as physics, chemistry, and math…     

Structural Data on the Periplasmic Aldehyde Oxidoreductase PaoABC from Escherichia coli: SAXS and Preliminary X-ray Crystallography Analysis

The periplasmic aldehyde oxidoreductase PaoABC from Escherichia coli is a molybdenum enzyme involved in detoxification of aldehydes in the cell. It is an example of an αβγ heterotrimeric enzyme of the xanthine oxidase family of enzymes which does not dimerize via its molybdenum cofactor binding domain. In order to structurally characterize PaoABC, X-ray crystallography and small angle X-ray scattering (SAXS) have been carried out. The protein crystallizes in the presence of 20% (w/v) polyethylene glycol 3350 using the hanging-drop vapour diffusion method. Although crystals were initially twinned, several experiments were done to overcome twinning and lowering the crystallization temperature (293 K to 277 K) was the solution to the problem. The non-twinned crystals used to solve the structure diffract X-rays to beyond 1.80 Å and belong to the C2 space group, with cell parameters a = 109.42 Å, b = 78.08 Å, c = 151.77 Å, β = 99.77°, and one molecule in the asymmetric unit. A molecular replacement solution was found for each subunit separately, using several proteins as search models. SAXS data of PaoABC were also collected showing that, in solution, the protein is also an αβγ heterotrimer.     

Small-Molecule Inhibitors of METTL3, the Major Human Epitranscriptomic Writer

The RNA methylase METTL3 catalyzes the transfer of a methyl group from the cofactor S-adenosyl-L-methionine (SAM) to the N⁶ atom of adenine. We have screened a library of 4000 analogues and derivatives of the adenosine moiety of SAM by high-throughput docking into METTL3. Two series of adenine derivatives were identified in silico, and the binding mode of six of the predicted inhibitors was validated by protein crystallography. Two compounds, one for each series, show good ligand efficiency. We propose a route for their further development into potent and selective inhibitors of METTL3.