Notch信号通路——对健康和疾病的机械论观点

The Notch signaling pathway is evolutionarily conserved across metazoan species and plays key roles in many physiological processes.The Notch receptor is activated by two families of canonical ligands(Deltalike and Serrate/Jagged)where both ligands and receptors are single-pass transmembrane proteins usually with large extracellular domains,relative to their intracellular portions.Upon interaction of the core binding regions,presented on opposing cell surfaces,formation of the receptor/ligand complex initiates force-mediated proteolysis,ultimately releasing the transcriptionally-active Notch intracellular domain.This review focuses on structural features of the extracellular receptor/ligand complex,the role of posttranslational modifications in tuning this complex,the contribution of the cell membrane to ligand function,and insights from acquired and genetic diseases.

Bionics and Structural Biology:A Novel Approach for Bio-energy Production

Cellular metabolism is a very complex process. The biochemical pathways are fundamental structures of biology. These pathways possess a number of regeneration steps which facilitate energy shuttling on a massive scale. This facilitates the biochemical pathways to sustain the energy currency of the cells. This concept has been mimicked using electronic circuit components and it has been used to increase the efficiency of bio-energy generation. Six of the carbohydrate biochemical pathways have been chosen in which glycolysis is the principle pathway. All the six pathways are interrelated and coordinated in a complex manner. Mimic circuits have been designed for all the six biochemical pathways. The components of the metabolic pathways such as enzymes, cofactors etc., are substituted by appropriate electronic circuit components. Enzymes are related to the gain of transistors by the bond dissociation energies of enzyme-substrate molecules under consideration. Cofactors and coenzymes are represented by switches and capacitors respectively. Resistors are used for proper orientation of the circuits. The energy obtained from the current methods employed for the decomposition of organic matter is used to trigger the mimic circuits. A similar energy shuttle is observed in the mimic circuits and the percentage rise for each cycle of circuit functioning is found to be 78.90. The theoretical calculations have been made using a sample of domestic waste weighing 1.182 kg. The calculations arrived at finally speak of the efficiency of the novel methodology employed.

Insights into the structural biology of G-protein coupled receptors impacts drug design for central nervous system neurodegenerative processes

In the last few years, there have been important new insights into the structural biology of G-protein coupled receptors. It is now known that allosteric binding sites are involved in the affinity and selec- tivity of ligands for G-protein coupled receptors, and that signaling by these receptors involves both G-protein dependent and independent pathways. The present review outlines the physiological and pharmacological implications of this perspective for the design of new drugs to treat disorders of the central nervous system. Specifically, new possibilities are explored in relation to allosteric and or- thosteric binding sites on dopamine receptors for the treatment of Parkinson＇s disease, and on muscarinic receptors for Alzheimer＇s disease. Future research can seek to identify ligands that can bind to more than one site on the same receptor, or simultaneously bind to two receptors and form a dimer. For example, the design of bivalent drugs that can reach homo/hetero-dimers of D2 dopa- mine receptor holds promise as a relevant therapeutic strategy for Parkinson＇s disease. Regarding the treatment of Alzheimer＇s disease, the design of dualsteric ligands for mono-oligomeric mus- carinic receptors could increase therapeutic effectiveness by generating potent compounds that could activate more than one signaling pathway.

Structural biology revolution led by technical breakthroughs in cryo-electron microscopy

Recent technical breakthroughs in cryo-electron microscopy（cryo-EM） revolutionized structural biology, which led to the 2017 Nobel Prize in chemistry being awarded to three scientists, Jacques Dubochet, Joachim Frank, and Richard Henderson, who made groundbreaking contributions to the development of cryo-EM. In this review, I will give a comprehensive review of the developmental history of cryo-EM, the technical aspects of the breakthrough in cryo-EM leading to the structural biology revolution, including electron microscopy, image recording devices and image processing algorithms,and the major scientific achievements by Chinese researchers employing cryo-EM, covering protein complexes involved in or related to gene expression and regulation, protein synthesis and degradation, membrane proteins, immunity, and viruses.Finally, I will give a perspective outlook on the development of cryo-EM in the future.

Zig, Zag, and ’Zyme: leveraging structural biology to engineer disease resistance

Dynamic host–pathogen interactions determine whether disease will occur.Pathogen effector proteins are central players in such disease development.On one hand,they improve susceptibility by manipulating host targets;on the other hand,they can trigger immunity after recognition by host immune receptors.A major research direction in the study of molecular plant pathology is to understand effector-host interactions,which has informed the development and breeding of crops with enhanced disease resistance.Recent breakthroughs on experiment-and artificial intelligence-based structure analyses significantly accelerate the development of this research area.Importantly,the detailed molecular insight of effector–host interactions enables precise engineering to mitigate disease.Here,we highlight a recent study by Xiao et al.,who describe the structure of an effector-receptor complex that consists of a fungal effector,with polygalacturonase(PG)activity,and a plant-derived polygalacturonase-inhibiting protein(PGIP).PGs weaken the plant cell wall and produce immune-suppressive oligogalacturonides(OGs)as a virulence mechanism;however,PGIPs directly bind to PGs and alter their enzymatic activity.When in a complex with PGIPs,PGs produce OG polymers with longer chains that can trigger immunity.Xiao et al.demonstrate that a PGIP creates a new active site tunnel,together with a PG,which favors the production of long-chain OGs.In this way,the PGIP essentially acts as both a PG receptor and enzymatic manipulator,converting virulence to defense activation.Taking a step forward,the authors used the PG-PGIP complex structure as a guide to generate PGIP variants with enhanced long-chain OG production,likely enabling further improved disease resistance.This study discovered a novel mechanism by which a plant receptor plays a dual role to activate immunity.It also demonstrates how fundamental knowledge,obtained through structural analyses,can be employed to guide the design of proteins with desired functions in agriculture.

An atypical ubiquitin ligase at the heart of neural development and programmed axon degeneration

The degeneration of nerve fibres following injury was first described by Augustus Waller over 170 years ago.Initially assumed to be a passive process,it is now evident that axons respond to insult via regulated cellular signaling events resulting in their programmed degeneration.Pro-survival and prodegenerative factors have been identified and their regulato ry mechanisms are beginning to emerge.The ubiquitin system has been implicated in the pro-degenerative process and a key component is the ubiquitin E3 ligase MYCBP2(also known as PHR1).Ubiquitin E3 ligases are tasked with the transfer of the small protein modifier ubiquitin to substrates and consist of hundreds of members.They can be classified as single subunit systems or as multi-subunit complexes.Their catalytic domains can also be assigned to three general architectures.Hints that MYCBP2 might not conform to these established formats came to light and it is now clear from biochemical and structural studies that MYCBP2 is indeed an outlier in terms of its modus operandi.Furthermore,the unconventional way in which MYCBP2 transfe rs ubiquitin to substrates has been linked to neurodevelopmental and pro-degenerative function.Herein,we will summarize these research developments relating to the unusual features of MYCBP2 and postulate therapeutic strategies that prevent Walle rian degeneration.These have exciting potential for providing relief from pathological neuropathies and neurodegenerative diseases.

Pyroptosis:Induction and inhibition strategies for immunotherapy of diseases

Cell death is a central process for organismal health.Pyroptosis,namely pyroptotic cell death,is recognized as a critical type that disrupts membrane and triggers pro-inflammatory cytokine secretion via gasdermins,providing a robust form of cytolysis.Meanwhile,along with the thorough research,a great deal of evidence has demonstrated the dual effects of pyroptosis in host defense and inflammatory diseases.More importantly,the recent identification of abundant gasdermin-like proteins in bacteria and fungi suggests an ancient origin of pyroptosis-based regulated cell death in the life evolution.In this review,we bring a general overview of pyroptosis pathways focusing on gasdermin structural biology,regulatory mechanisms,and recent progress in induction and inhibition strategies for disease treatment.We look forward to providing an insightful perspective for readers to comprehend the frame and challenges of the pyroptosis field,and to accelerating its clinical application.

The structural biology of ryanodine receptors

Ryanodine receptors are ion channels that allow for the release of Ca2+ from the endoplasmic or sarcoplasmic reticulum.They are expressed in many different cell types but are best known for their predominance in skeletal and cardiac myocytes,where they are directly involved in excitation-contraction coupling.With molecular weights exceeding 2 MDa,Ryanodine Receptors are the largest ion channels known to date and present major challenges for structural biology.Since their discovery in the 1980s,significant progress has been made in understanding their behaviour through multiple structural methods.Cryo-electron microscopy reconstructions of intact channels depict a mushroom-shaped structure with a large cytoplasmic region that pre-sents many binding sites for regulatory molecules.This region undergoes significant motions during opening and closing of the channel,demonstrating that the Ryanodine Receptor is a bona fide allosteric protein.High-resolution structures through X-ray crystallography and NMR currently cover～11% of the entire protein.The combination of high-and low-resolution methods allows us to build pseudo-atomic models.Here we present an overview of the electron microscopy,NMR,and crystallographic analyses of this membrane protein giant.

The recombinant expression systems for structure determination of eukaryotic membrane proteins

Eukaryotic membrane proteins, many of which are key players in various biological processes, constitute more than half of the drug targets and represent important candidates for structural studies. In contrast to their physiological significance, only very limited number of eukaryoUc membrane protein structures have been obtained due to the technical challenges in the genera- tion of recombinant proteins. In this review, we examine the major recombinant expression systems for eukaryotic membrane proteins and compare their relative advantages and disadvantages. We also attempted to summarize the recent technical strategies in the advancement of eukaryotic membrane protein purification and crystallization.

Cryo-electron microscopy for structural biology:current status and future perspectives

Recently, significant technical breakthroughs in both hardware equipment and software algorithms have enabled cryo-electron microscopy(cryo-EM) to become one of the most important techniques in biological structural analysis. The technical aspects of cryo-EM define its unique advantages and the direction of development. As a rapidly emerging field, cryo-EM has benefitted from highly interdisciplinary research efforts. Here we review the current status of cryo-EM in the context of structural biology and discuss the technical challenges. It may eventually merge structural and cell biology at multiple scales.

Structural biology of the macroautophagy machinery

Macroautophagy is a conserved degradative process mediated through formation of a unique double- membrane structure, the autophagosome. The discovery of autophagy-related （Atg） genes required for autophagosome formation has led to the characterization of approximately 20 genes mediating this process. Recent structural studies of the Atg proteins have provided the molecular basis for their function. Here we summarize the recent progress in elucidating the structural basis for autophagosome formation.

Crystal structure of Arabidopsis thaliana HPPK/DHPS,a bifunctional enzyme and target of the herbicide asulam

Herbicides are vital formodern agriculture,but their utility is threatened by genetic or metabolic resistance in weeds,as well as regulatory barriers.Of the known herbicide modes of action,7,8-dihydropterin synthase(DHPS),which is involved in folate biosynthesis,is targeted by just one commercial herbicide,asulam.A mimic of the substrate para-aminobenzoic acid,asulam is chemically similar to sulfonamide antibiotics,and although it is still in widespread use,asulam has faced regulatory scrutiny.With an entire mode of action represented by just one commercial agrochemical,we sought to improve the understanding of its plant target.Here we solve a 2.3A°resolution crystal structure for Arabidopsis thaliana DHPS that is conjoined to 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase(HPPK),and we reveal a strong structural conservation with bacterial counterparts at the sulfonamide-bindingpocket of DHPS.We demonstrate that asulamand the antibiotic sulfamethoxazole have herbicidal as well as antibacterial activity,andwe explore the structural basis of their potency by modeling these compounds in mitochondrial HPPK/DHPS.Our findings suggest limited opportunity for the rational design of plant selectivity fromasulamand indicate that pharmacokinetic or delivery differences between plants andmicrobesmight be the bestways to safeguard thismode of action.

Combination of NMR spectroscopy and X-ray crystallography offers unique advantages for elucidation of the structural basis of protein complex assembly

NMR spectroscopy and X-ray crystallography are two premium methods for determining the atomic structures of macro-biomolecular complexes.Each method has unique strengths and weaknesses.While the two techniques are highly complementary,they have generally been used separately to address the structure and functions of biomolecular complexes.In this review,we emphasize that the combination of NMR spectroscopy and X-ray crystallography offers unique power for elucidating the structures of complicated protein assemblies.We demonstrate,using several recent examples from our own laboratory,that the exquisite sensitivity of NMR spectroscopy in detecting the conformational properties of individual atoms in proteins and their complexes,without any prior knowledge of conformation,is highly valuable for obtaining the high quality crystals necessary for structure determination by X-ray crystallography.Thus NMR spectroscopy,in addition to answering many unique structural biology questions that can be addressed specifically by that technique,can be exceedingly powerful in modern structural biology when combined with other techniques including X-ray crystallography and cryo-electron microscopy.

Cryo-EM for nanomaterials:Progress and perspective

Cryogenic electron microscopy(cryo-EM)has extensively boosted structural biology research since the“resolution revolution”in the year of 2013 which was soon awarded the Nobel Prize in Chemistry in 2017.The advances in camera techniques and software algorithms enabled cryoEM to routinely characterize the three-dimensional structures of biomolecules at near-atomic resolution.Biomolecules are basically sensitive to electron irradiation damage,which can be minimized at cryo-temperature.This principle has inspired material scientists to characterize electron beam-or air-sensitive materials by cryo-EM,such as the electrodes in the lithium-ion battery,metal-organic frameworks(MOFs),covalent-organic frameworks(COFs)and zeolites.In addition,the reaction systems can be fast-frozen at vitreous ice in cryoEM,which correspondingly preserves the materials at the close-to-native state.Herein,we summarized the development and applications of both the cryo-EM technique and other emerging cryo-techniques in materials science,and energy storage and conversion.Cryo-EM techniques,capable of the direct observation of sensitive materials and electrochemical reaction processes,will greatly renew our understanding of materials science and related mechanisms.

The structural basis for glycerol permeation by human AQP7

Human glycerol channel aquaporin 7(AQP7)conducts glycerol release from adipocyte and enters the cells in pancreatic islets,muscles,and kidney tubules,and thus regulates glycerol metabolism in those tissues.Compared with other human aquaglyceroporins,AQP7 shows a less conserved‘‘NPA”motif in the center cavity and a pair of aromatic residues at Ar/R selectivity filter.To understand the structural basis for the glycerol conductance,we crystallized the human AQP7 and determined the structure at 3.7Å.A substrate binding pocket was found near the Ar/R filter where a glycerol molecule is bound and stabilized by R229.Glycerol uptake assay on human AQP7 as well as AQP3 and AQP10 demonstrated strong glycerol transportation activities at the physiological condition.The human AQP7 structure,in combination with the molecular dynamics simulation thereon,reveals a fully closed conformation with its permeation pathway strictly confined by the Ar/R filter at the exoplasmic side and the gate at the cytoplasmic side,and the binding of glycerol at the Ar/R filter plays a critical role in controlling the glycerol flux by driving the dislocation of the residues at narrowest parts of glycerol pathway in AQP7.

On the necessity of an integrative approach to understand protein structural dynamics

Proteins are dynamic,fluctuating between multiple conformational states.Protein dynamics,spanning orders of magnitude in time and space,allow proteins to perform specific functions.Moreover,under certain conditions,proteins can morph into a different set of conformations.Thus,a complete understanding of protein structural dynamics can provide mechanistic insights into protein function.Here,we review the latest developments in methods used to determine protein ensemble structures and to characterize protein dynamics.Techniques including X-ray crystallography,cryogenic electron microscopy,and small angle scattering can provide structural information on specific conformational states or on the averaged shape of the protein,whereas techniques including nuclear magnetic resonance,fluorescence resonance energy transfer(FRET),and chemical cross-linking coupled with mass spectrometry provide information on the fluctuation of the distances between protein domains,residues,and atoms for the multiple conformational states of the protein.In particular,FRET measurements at the single-molecule level allow rapid resolution of protein conformational states,where information is otherwise obscured in bulk measurements.Taken together,the different techniques complement each other and their integrated use can offer a clear picture of protein structure and dynamics.