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...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.展开更多
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...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.展开更多
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 Fran...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.展开更多
From cracking the code of viruses to mentoring the next generation of scientists,the former president of Nankai University has contributed a lot to turning microscopic discoveries into monumental shields for global he...From cracking the code of viruses to mentoring the next generation of scientists,the former president of Nankai University has contributed a lot to turning microscopic discoveries into monumental shields for global health.OVER the past 40 years,one man has distinguished himself through a deep commitment to researching protein structures of high pathogenic viruses,and published numerous significant works in top international scientific journals.展开更多
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 skele...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.展开更多
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 a...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.展开更多
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 forma...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.展开更多
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;...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.展开更多
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,pr...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.展开更多
A recent study led by Yi-Wei Chang1,published in Science,integrates cryo-electron single-particle analysis(SPA)and cryo-electron tomography(cryo-ET)to elucidate the near-atomic architecture of the influenza virus ribo...A recent study led by Yi-Wei Chang1,published in Science,integrates cryo-electron single-particle analysis(SPA)and cryo-electron tomography(cryo-ET)to elucidate the near-atomic architecture of the influenza virus ribonucleoprotein(RNP)complex.The study reveals that the RNP adopts a right-handed,antiparallel double-helical configuration,in which the viral RNA is translocated via a polymerase-driven strand sliding mechanism.Dynamic tail loop interactions between adjacent nucleoprotein(NP)subunits impart structural flexibility to the RNP,enabling conformational dynamics essential for processive RNA synthesis.These findings define a structural basis for strand sliding,and guided by this insight,the authors identify novel small molecules that disrupt NP–NP interactions by targeting a conserved tail loop interface,laying a foundation for broad-spectrum influenza antivirals.展开更多
In the year 1971,the world’s biggest structural biology collaboration name—The Research Collaboratory for Structural Bioinformatics(RCSB),was formed to gather all the structural biologists at a single platform and t...In the year 1971,the world’s biggest structural biology collaboration name—The Research Collaboratory for Structural Bioinformatics(RCSB),was formed to gather all the structural biologists at a single platform and then extended out to be the world’s most extensive structural data repository named RCSB-Protein Data Bank(PDB)(https://www.rcsb.org/)that has provided the service for more than 50 years and continues its legacy for the discoveries and repositories for structural data.The RCSB has evolved from being a collaboratory network to a full-fledged database and tool with a huge list of protein structures,nucleic acid-containing structures,ModelArchive,and AlphaFold structures,and the best is that it is expanding day by day with computational advancement with tools and visual experiences.In this review article,we have discussed how RCSB has been a successful collaboratory network,its expansion in each decade,and how it has helped the ground-breaking research.The PDB tools that are helping the researchers,yearly data deposition,validation,processing,and suggestions that can help the developer improve for upcoming years are also discussed.This review will help future researchers understand the complete history of RCSB and its developments in each decade and how various future collaborative networks can be developed in various scientific areas and can be successful by keeping RCSB as a case study.展开更多
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 Se...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.展开更多
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 cellul...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.展开更多
Somatostatin receptor 1(SSTR1)is a crucial therapeutic target for various neuroendocrine and oncological disorders.Current SSTR1-targeted treatments,including the first-generation somatostatin analog lanreotide(Lan)an...Somatostatin receptor 1(SSTR1)is a crucial therapeutic target for various neuroendocrine and oncological disorders.Current SSTR1-targeted treatments,including the first-generation somatostatin analog lanreotide(Lan)and the second-generation analog pasireotide(Pas),show promise but encounter challenges related to selectivity and efficacy.This study presents high-resolution cryo-electron microscopy structures of SSTR1 complexed with Lan or Pas,revealing the distinct mechanisms of ligand-binding and activation.These structures illustrate unique conformational changes in the SSTR1 orthosteric pocket induced by each ligand,which are critical for receptor activation and ligand selectivity.Combined with the biochemical assays and molecular dynamics simulations,our results provide a comparative analysis of binding characteristics within the SSTR family,highlighting subtle differences in SSTR1 activation by Lan and Pas.These insights pave the way for designing next-generation therapies with enhanced efficacy and reduced side effects through improved receptor subtype selectivity.展开更多
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 wi...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.展开更多
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 hig...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.展开更多
Hornworts are the only land plants that employ a pyrenoid to optimize Rubisco’s CO_(2) fixation,yet hornwort Rubisco remains poorly characterized.Here we assembled the hornwort Anthoceros agrestis Rubisco(AaRubisco)u...Hornworts are the only land plants that employ a pyrenoid to optimize Rubisco’s CO_(2) fixation,yet hornwort Rubisco remains poorly characterized.Here we assembled the hornwort Anthoceros agrestis Rubisco(AaRubisco)using the Arabidopsis thaliana SynBio expression system and observed the formation of stalled intermediates,prompting us to develop a new SynBio system with A.agrestis cognate chaperones.We successfully assembled AaRubisco and Rubisco from three other hornwort species.Unlike A.thaliana Rubisco,AaRubisco assembly is not dependent on RbcX or Raf2.Kinetic characterization reveals that hornwort Rubiscos exhibit a range of catalytic rates(3–10 s−1),but with similar affinity(∼30μM)and specificity(∼70)for CO_(2).These results suggest that hornwort Rubiscos do not comply with the long-held canonical catalytic trade-off observed in other land plants,providing experimental support that Rubisco kinetics may be phylogenetically constrained.Unexpectedly,we observed a 50%increase in AaRubisco catalytic rates when RbcX was removed from our SynBio system,without any reduction in specificity.Structural biology,biochemistry,and proteomic analysis suggest that subtle differences in Rubisco large-subunit interactions,when RbcX is absent during biogenesis,increases the accessibility of active sites and catalytic turnover rate.Collectively,this study uncovered a previously unknown Rubisco kinetic parameter space and provides a SynBio chassis to expand the survey of other Rubisco kinetics.Our discoveries will contribute to developing new approaches for engineering Rubisco with superior kinetics.展开更多
Editor’s note This manuscript offers a significant conceptual advance by addressing the long-standing challenge of calcitonin tachyphylaxis through an innovative evolutionary framework.Rather than an incremental find...Editor’s note This manuscript offers a significant conceptual advance by addressing the long-standing challenge of calcitonin tachyphylaxis through an innovative evolutionary framework.Rather than an incremental finding,it reframes the problem by proposing that insights can be drawn from a naturally superior system in fish.It effectively bridges distinct,high-impact fields-evolutionary biology,structural biology,and translational medicine-providing both the“why”and the“how”behind the mechanistic differences.Furthermore,it outlines clear,actionable research strategies,such as designing stableα-helical calcitonin analogs,developing RAMP-agnostic modulators,and using peptides to disrupt the RAMP-CTR interface,which are likely to inspire and direct future experimental and therapeutic efforts.Given its direct relevance to unresolved clinical issues in osteoporosis,Paget s disease,and hypercalcemia,the work is poised to attract immediate interest from clinical endocrinologists and bone biologists.Its integrative and hypothesis-generating nature makes it a key reference in review articles across GPCR biology,evolutionary medicine,and bone therapeutics.展开更多
The plant immune system relies on a precisely balanced interplay between activation and repression to effectively combat pathogens without incurring self-damage.The salicylic acid(SA)signaling pathway,a cornerstone of...The plant immune system relies on a precisely balanced interplay between activation and repression to effectively combat pathogens without incurring self-damage.The salicylic acid(SA)signaling pathway,a cornerstone of this system,is currently experiencing a research renaissance.Landmark studies have recently elucidated the complete enzymatic pathways for SA biosynthesis from both chorismate and phenylalanine(Liu et al.,2025;Wang et al.,2025;Zhu et al.,2025),while advances in structural biology have resolved the atomic-level architecture of key signaling components(Kumar et al.,2022).展开更多
Nicotinamide mononucleotide(NMN)is a nucleotide of significant biological importance,found abundantly in various foods such as meat,fruits,and vegetables.Recently,its potential effects in delaying aging have attracted...Nicotinamide mononucleotide(NMN)is a nucleotide of significant biological importance,found abundantly in various foods such as meat,fruits,and vegetables.Recently,its potential effects in delaying aging have attracted considerable attention.Although chemical synthesis methods are commonly employed,they do not align with green production standards.In contrast,the biosynthesis of NMN is both safer and more environmentally sus-tainable.In this review,we established a novel“substrate-pathway-enzymology”framework to analyze the research on NMN biosynthesis.First,we systematically trace four substrates(nicotinamide ribose,nicotinamide,niacin,and nicotinamide adenine dinucleotide)and their respective metabolic routes.Then,we thoroughly investigate key enzymes through structural biology and protein engineering approaches,and converge the fragmented research findings across pathways to construct a comprehensive NMN biosynthesis network,revealing intricate metabolic regulations and pathway interactions.Through comparative analysis,the most promising biosynthetic pathway and prospects are discussed.Additionally,this review also provides original perspectives for NMN industrial development.展开更多
文摘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.
基金supported by SIP-IPN,CONACYT (CB-168116)FIS/IMSS (FIS/IMSS/PROT/G11-2/1013)
文摘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.
基金Project supported by the National Key Research and Development Program of China(Grant No.2017YFA0504700)the National Natural Science Foundation of China(Grant Nos.31570732 and 31770785)
文摘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.
文摘From cracking the code of viruses to mentoring the next generation of scientists,the former president of Nankai University has contributed a lot to turning microscopic discoveries into monumental shields for global health.OVER the past 40 years,one man has distinguished himself through a deep commitment to researching protein structures of high pathogenic viruses,and published numerous significant works in top international scientific journals.
基金funded by the CIHR(operating grant 84350)the Heart and Stroke Foundation of Canadaa CIHR new investigator and a Michael Smith Foundation for Health Research Scholar
文摘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.
文摘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.
文摘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.
基金supported by Gatsby Charitable Foundation and UKRI BBSRC Grant BBS/E/J/000PR9797.
文摘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.
基金supported by the National Key R&D Program of China(No.2018YFA0507700)
文摘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.
基金supported by the Key Research and Development Program,Ministry of Science and Technology of the People's Republic of China(No.2023YFC2606500).
文摘A recent study led by Yi-Wei Chang1,published in Science,integrates cryo-electron single-particle analysis(SPA)and cryo-electron tomography(cryo-ET)to elucidate the near-atomic architecture of the influenza virus ribonucleoprotein(RNP)complex.The study reveals that the RNP adopts a right-handed,antiparallel double-helical configuration,in which the viral RNA is translocated via a polymerase-driven strand sliding mechanism.Dynamic tail loop interactions between adjacent nucleoprotein(NP)subunits impart structural flexibility to the RNP,enabling conformational dynamics essential for processive RNA synthesis.These findings define a structural basis for strand sliding,and guided by this insight,the authors identify novel small molecules that disrupt NP–NP interactions by targeting a conserved tail loop interface,laying a foundation for broad-spectrum influenza antivirals.
文摘In the year 1971,the world’s biggest structural biology collaboration name—The Research Collaboratory for Structural Bioinformatics(RCSB),was formed to gather all the structural biologists at a single platform and then extended out to be the world’s most extensive structural data repository named RCSB-Protein Data Bank(PDB)(https://www.rcsb.org/)that has provided the service for more than 50 years and continues its legacy for the discoveries and repositories for structural data.The RCSB has evolved from being a collaboratory network to a full-fledged database and tool with a huge list of protein structures,nucleic acid-containing structures,ModelArchive,and AlphaFold structures,and the best is that it is expanding day by day with computational advancement with tools and visual experiences.In this review article,we have discussed how RCSB has been a successful collaboratory network,its expansion in each decade,and how it has helped the ground-breaking research.The PDB tools that are helping the researchers,yearly data deposition,validation,processing,and suggestions that can help the developer improve for upcoming years are also discussed.This review will help future researchers understand the complete history of RCSB and its developments in each decade and how various future collaborative networks can be developed in various scientific areas and can be successful by keeping RCSB as a case study.
基金supported by the Medical Research Council (MRC)Grant (MR/V008935/1)supported by the National Natural Science Foundation of China (82304596)+2 种基金the Fundamental Research Funds for the Central Universities (3332022057)the CAMS Innovation Fund for Medical Sciences (2022-I2M-1-016)supported by the National Natural Science Foundation of China (81973383).
文摘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.
基金the United Kingdom MRC(MC_UU_12016/8)the Biotechnology and Biological Sciences Research Council(BB/P003982/1)The Michael J.Fox Foundation(to SV)。
文摘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.
基金supported by funds from the Ganghong Young Scholar Development Fund(China)and the Shenzhen-Hong Kong Cooperation Zone for Technology and Innovation(No.HZQB-KCZYB-2020056,China)Thiansze Wong is supported by research fundings from Shenzhen Pengcheng Peacock Plan(Nos.2021TC0059 and 2024TC0153,China)+7 种基金Yang Du is supported by grants from the National Natural Science Foundation of China(No.32271263)Shenzhen Sci.&Tech Innovation Bureau(Nos.JCYJ 20220818103009018 and JCYJ 20240813113521028,China)and the Shenzhen-Hong Kong Cooperation Zone for Technology and Innovation(No.HZQB-KCZYB-2020056,China)Richard Ye is supported by Shenzhen Medical Research Fund(No.SMRFD2403009,China)Joint Research Fund of the Second Affiliated Hospital-School of Medicine,the Chinese University of Hong Kong,Shenzhen(No.YXLH13,China)Ganghong Young Scholar Development Fund(No.2019E0020)and Fund from Shenzhen-Hong Kong Cooperation Zone for Technology and Innovation(No.HZQB-KCZYB-2020056,China)Jing Chen is supported by the National Natural Science Foundation of China(No.31271243)。
文摘Somatostatin receptor 1(SSTR1)is a crucial therapeutic target for various neuroendocrine and oncological disorders.Current SSTR1-targeted treatments,including the first-generation somatostatin analog lanreotide(Lan)and the second-generation analog pasireotide(Pas),show promise but encounter challenges related to selectivity and efficacy.This study presents high-resolution cryo-electron microscopy structures of SSTR1 complexed with Lan or Pas,revealing the distinct mechanisms of ligand-binding and activation.These structures illustrate unique conformational changes in the SSTR1 orthosteric pocket induced by each ligand,which are critical for receptor activation and ligand selectivity.Combined with the biochemical assays and molecular dynamics simulations,our results provide a comparative analysis of binding characteristics within the SSTR family,highlighting subtle differences in SSTR1 activation by Lan and Pas.These insights pave the way for designing next-generation therapies with enhanced efficacy and reduced side effects through improved receptor subtype selectivity.
基金the National Key Research and Development Program of China(2018YFC1004704 and 2017YFC1001303)the National Natural Science Foundation of China(U1632132,31670849,and 91853206)+3 种基金the Shanghai Science and Technology Committee(20S11902000)the SHIPM-pi fund(JY201804)the SHIPM-sigma fund(2018JC002)from Shanghai Institute of Precision Medicine,Ninth People’s Hospital Shanghai Jiao Tong University School of Medicinethe Innovative Research Team of Highlevel Local Universities in Shanghai(SSMU-ZLCX20180600)。
文摘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.
基金supported by grants from the Research Grants Council of Hong Kong to M.Z.supported by the National Major Basic Research Program of China (Grant No. 2011CB910500)+3 种基金the National Natural Science Foundation of China (Grant No. 31070657)the Knowledge Innovation Program of the Chinese Academy of Sciences (Grant No. KSCX2-YW-R-154)The NMR spectrometers used in our studies were funded by donations from the Hong Kong Jockey Club Charity Foundationthe Special Equipment Grant from RGC of Hong Kong (Grant No. SEG_HKUST06)
文摘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.
基金National Science Foundation grant no.MCB-2213840 to L.H.G.and MCB-2213841 to F.-W.L.
文摘Hornworts are the only land plants that employ a pyrenoid to optimize Rubisco’s CO_(2) fixation,yet hornwort Rubisco remains poorly characterized.Here we assembled the hornwort Anthoceros agrestis Rubisco(AaRubisco)using the Arabidopsis thaliana SynBio expression system and observed the formation of stalled intermediates,prompting us to develop a new SynBio system with A.agrestis cognate chaperones.We successfully assembled AaRubisco and Rubisco from three other hornwort species.Unlike A.thaliana Rubisco,AaRubisco assembly is not dependent on RbcX or Raf2.Kinetic characterization reveals that hornwort Rubiscos exhibit a range of catalytic rates(3–10 s−1),but with similar affinity(∼30μM)and specificity(∼70)for CO_(2).These results suggest that hornwort Rubiscos do not comply with the long-held canonical catalytic trade-off observed in other land plants,providing experimental support that Rubisco kinetics may be phylogenetically constrained.Unexpectedly,we observed a 50%increase in AaRubisco catalytic rates when RbcX was removed from our SynBio system,without any reduction in specificity.Structural biology,biochemistry,and proteomic analysis suggest that subtle differences in Rubisco large-subunit interactions,when RbcX is absent during biogenesis,increases the accessibility of active sites and catalytic turnover rate.Collectively,this study uncovered a previously unknown Rubisco kinetic parameter space and provides a SynBio chassis to expand the survey of other Rubisco kinetics.Our discoveries will contribute to developing new approaches for engineering Rubisco with superior kinetics.
文摘Editor’s note This manuscript offers a significant conceptual advance by addressing the long-standing challenge of calcitonin tachyphylaxis through an innovative evolutionary framework.Rather than an incremental finding,it reframes the problem by proposing that insights can be drawn from a naturally superior system in fish.It effectively bridges distinct,high-impact fields-evolutionary biology,structural biology,and translational medicine-providing both the“why”and the“how”behind the mechanistic differences.Furthermore,it outlines clear,actionable research strategies,such as designing stableα-helical calcitonin analogs,developing RAMP-agnostic modulators,and using peptides to disrupt the RAMP-CTR interface,which are likely to inspire and direct future experimental and therapeutic efforts.Given its direct relevance to unresolved clinical issues in osteoporosis,Paget s disease,and hypercalcemia,the work is poised to attract immediate interest from clinical endocrinologists and bone biologists.Its integrative and hypothesis-generating nature makes it a key reference in review articles across GPCR biology,evolutionary medicine,and bone therapeutics.
基金supported by grants from the United States Department of Agriculture National Institute of Food and Agriculture(ECDRE 2022-70029-38470 and ECDRE 2025-70029-44031 to Z.M.)by a scholarship from the University of Florida Plant Molecular and Cellular Biology Program(to M.Z.).
文摘The plant immune system relies on a precisely balanced interplay between activation and repression to effectively combat pathogens without incurring self-damage.The salicylic acid(SA)signaling pathway,a cornerstone of this system,is currently experiencing a research renaissance.Landmark studies have recently elucidated the complete enzymatic pathways for SA biosynthesis from both chorismate and phenylalanine(Liu et al.,2025;Wang et al.,2025;Zhu et al.,2025),while advances in structural biology have resolved the atomic-level architecture of key signaling components(Kumar et al.,2022).
基金supposed by the Talent Introduction Program at Chengdu University of Traditional Chinese Medicine(030041227).
文摘Nicotinamide mononucleotide(NMN)is a nucleotide of significant biological importance,found abundantly in various foods such as meat,fruits,and vegetables.Recently,its potential effects in delaying aging have attracted considerable attention.Although chemical synthesis methods are commonly employed,they do not align with green production standards.In contrast,the biosynthesis of NMN is both safer and more environmentally sus-tainable.In this review,we established a novel“substrate-pathway-enzymology”framework to analyze the research on NMN biosynthesis.First,we systematically trace four substrates(nicotinamide ribose,nicotinamide,niacin,and nicotinamide adenine dinucleotide)and their respective metabolic routes.Then,we thoroughly investigate key enzymes through structural biology and protein engineering approaches,and converge the fragmented research findings across pathways to construct a comprehensive NMN biosynthesis network,revealing intricate metabolic regulations and pathway interactions.Through comparative analysis,the most promising biosynthetic pathway and prospects are discussed.Additionally,this review also provides original perspectives for NMN industrial development.
