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structure, function, and Propagation of Information across Living Two, Four, and Eight Node Degree Topologies

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY 2016年第0期4卷 15-15页

作者： Alagapan, Sankaraleengam Franca, Eric Pan, Liangbin Leondopulos, Stathis Wheeler, Bruce C. DeMarse, Thomas B. Univ Florida J Crayton Pruitt Family Dept Biomed Engn Gainesville FL 32611 USA Univ Calif San Diego Dept Biomed Engn San Diego CA 92103 USA Univ Florida Dept Pediat Neurol Gainesville FL 32611 USA

In this study, we created four network topologies composed of living cortical neurons and compared resultant structural-functional dynamics including the nature and quality of information transmission. Each living network was composed of living cortical neurons and were created using microstamping of adhesion promoting molecules and each was "designed" with different levels of convergence embedded within each structure. Networks were cultured over a grid of electrodes that permitted detailed measurements of neural activity at each node in the network. Of the topologies we tested, the "Random" networks in which neurons connect based on their own intrinsic properties transmitted information embedded within their spike trains with higher fidelity relative to any other topology we tested. Within our patterned topologies in which we explicitly manipulated structure, the effect of convergence on fidelity was dependent on both topology and time-scale (rate vs. temporal coding). A more detailed examination using tools from network analysis revealed that these changes in fidelity were also associated with a number of other structural properties including a node's degree, degree-degree correlations, path length, and clustering coefficients. Whereas information transmission was apparent among nodes with few connections, the greatest transmission fidelity was achieved among the few nodes possessing the highest number of connections (high degree nodes or putative hubs). These results provide a unique view into the relationship between structure and its affect on transmission fidelity, at least within these small neural populations with defined network topology. They also highlight the potential role of tools such as microstamp printing and microelectrode array recordings to construct and record from arbitrary network topologies to provide a new direction in which to advance the study of structure-function relationships.

关键词： structure-function information transmission convergence-divergence graph theory cortical networks

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Diversity of function and higher-order structure within HWE sensor histidine kinases

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JOURNAL OF BIOLOGICAL CHEMISTRY 2023年第8期299卷 104934页

作者： Dikiy, Igor Swingle, Danielle Toy, Kaitlyn Edupuganti, Uthama R. Rivera-Cancel, Giomar Gardner, Kevin H. CUNY Adv Sci Res Ctr Struct Biol Initiat New York NY 10031 USA CUNY Grad Ctr PhD Program Biochem New York NY 10031 USA CUNY City Coll Dept Chem & Biochem New York NY 10031 USA UT Southwestern Med Ctr Dept Internal Med Dallas TX USA CUNY Grad Ctr PhD Program Biol & Chem New York NY 10031 USA

Integral to the protein structure/function paradigm, oligomeric state is typically conserved along with function across evolution. However, notable exceptions such as the hemoglobins show how evolution can alter oligomerization to enable new regulatory mechanisms. Here, we examine this linkage in histidine kinases (HKs), a large class of widely distributed prokaryotic environmental sensors. While the majority of HKs are transmembrane homodimers, members of the HWE/HisKA2 family can deviate from this architecture as exemplified by our finding of a monomeric soluble HWE/HisKA2 HK (EL346, a photosensing light-oxygen-voltage [LOV]-HK). To further explore the diversity of oligomerization states and regulation within this family, we biophysically and biochemically characterized multiple EL346 homologs and found a range of HK oligomeric states and functions. Three LOV-HK homologs are primarily dimeric with differing structural and functional responses to light, while two Per-ARNT-Sim-HKs interconvert between differentially active monomers and dimers, suggesting dimerization might control enzymatic activity for these proteins. Finally, we examined putative interfaces in a dimeric LOV-HK, finding that multiple regions contribute to dimerization. Our findings suggest the potential for novel regulatory modes and oligomeric states beyond those traditionally defined for this important family of environmental sensors.

关键词： histidine kinase bacterial signal transduction conformational change structure-function biophysics environmental sensing two-component system HWE family HisKA2 family

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The Odyssey of a Young Gene: structure-function Studies in Human Glutamate Dehydrogenases Reveal Evolutionary-Acquired Complex Allosteric Regulation Mechanisms

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NEUROCHEMICAL RESEARCH 2014年第3期39卷 471-486页

作者： Zaganas, Ioannis V. Kanavouras, Konstantinos Borompokas, Nikolas Arianoglou, Giovanna Dimovasili, Christina Latsoudis, Helen Vlassi, Metaxia Mastorodemos, Vasileios Univ Crete Neurol Lab Sch Med Iraklion 71003 Crete Greece Natl Ctr Sci Res Demokritos Inst Biosci & Applicat Athens 15310 Greece

Mammalian glutamate dehydrogenase (GDH) catalyzes the reversible inter-conversion of glutamate to alpha-ketoglutarate and ammonia, interconnecting carbon skeleton and nitrogen metabolism. In addition, it functions as an energy switch by its ability to fuel the Krebs cycle depending on the energy status of the cell. As GDH lies at the intersection of several metabolic pathways, its activity is tightly regulated by several allosteric compounds that are metabolic intermediates. In contrast to other mammals that have a single GDH-encoding gene, humans and great apes possess two isoforms of GDH (hGDH1 and hGDH2, encoded by the GLUD1 and GLUD2 genes, respectively) with distinct regulation pattern, but remarkable sequence similarity (they differ, in their mature form, in only 15 of their 505 amino-acids). The GLUD2 gene is considered a very young gene, emerging from the GLUD1 gene through retro-position only recently (< 23 million years ago). The new hGDH2 iso-enzyme, through random mutations and natural selection, is thought to have conferred an evolutionary advantage that helped its persistence through primate evolution. The properties of the two highly homologous human GDHs have been studied using purified recombinant hGDH1 and hGDH2 proteins obtained by expression of the corresponding cDNAs in Sf21 cells. According to these studies, in contrast to hGDH1 that maintains basal activity at 35-40 % of its maximal, hGDH2 displays low basal activity that is highly responsive to activation by rising levels of ADP and/or l-leucine which can also act synergistically. While hGDH1 is inhibited potently by GTP, hGDH2 shows remarkable GTP resistance. Furthermore, the two iso-enzymes are differentially inhibited by estrogens, polyamines and neuroleptics, and also differ in heat-lability. To elucidate the molecular mechanisms that underlie these different regulation patterns of the two iso-enzymes (and consequently the evolutionary adaptation of hGDH2 to a new functional role), we hav

关键词： Glutamate dehydrogenase hGDH1 hGDH2 Evolution Enzyme regulation structure-function

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Relating structure and function of inner hair cell ribbon synapses

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CELL AND TISSUE RESEARCH 2015年第1期361卷 95-114页

作者： Wichmann, C. Moser, T. Univ Med Ctr Gottingen Inst Auditory Neurosci Mol Architecture Synapses Grp Gottingen Germany Univ Med Ctr Gottingen InnerEarLab Gottingen Germany Univ Med Ctr Gottingen Collaborat Res Ctr 889 Gottingen Germany Univ Med Ctr Gottingen Inst Auditory Neurosci Gottingen Germany Univ Gottingen Ctr Nanoscale Microscopy & Mol Physiol Brain D-37073 Gottingen Germany Univ Gottingen Bernstein Ctr Computat Neurosci D-37073 Gottingen Germany

In the mammalian cochlea, sound is encoded at synapses between inner hair cells (IHCs) and type I spiral ganglion neurons (SGNs). Each SGN receives input from a single IHC ribbon-type active zone (AZ) and yet SGNs indefatigably spike up to hundreds of Hz to encode acoustic stimuli with submillisecond precision. Accumulating evidence indicates a highly specialized molecular composition and structure of the presynapse, adapted to suit these high functional demands. However, we are only beginning to understand key features such as stimulus-secretion coupling, exocytosis mechanisms, exo-endocytosis coupling, modes of endocytosis and vesicle reformation, as well as replenishment of the readily releasable pool. Relating structure and function has become an important avenue in addressing these points and has been applied to normal and genetically manipulated hair cell synapses. Here, we review some of the exciting new insights gained from recent studies of the molecular anatomy and physiology of IHC ribbon synapses.

关键词： structure-function Inner hair cells Ribbon synapse Exo-endocytosis Otoferlin

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Patchwork structure-function analysis of the Sendai virus matrix protein

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VIROLOGY 2014年第1期464卷 330-340页

作者： Mottet-Osman, Genevieve Miazza, Vincent Vidalain, Pierre-Olivier Roux, Laurent Univ Geneva Dept Microbiol & Mol Med Fac Med Geneva Switzerland Inst Pasteur CNRS UMR3569 Viral Genom & Vaccinat Unit Paris France

Paramyxoviruses contain a bi-lipidic envelope decorated by two transmembrane glycoproteins and carpeted on the inner surface with a layer of matrix proteins (M), thought to bridge the glycoproteins with the viral nucleocapsids. To characterize M structure-function features, a set of M domains were mutated or deleted. The genes encoding these modified M were incorporated into recombinant Sendai viruses and expressed as supplemental proteins. Using a method of integrated suppression complementation system (ISCS), the functions of these M mutants were analyzed in the context of the infection. Cellular membrane association, localization at the cell periphery, nucleocapsid binding, cellular protein interactions and promotion of viral particle formation were characterized in relation with the mutations. At the end, lack of nucleocapsid binding go together with lack of cell surface localization and both features definitely correlate with loss of M global function estimated by viral particle production. (C) 2014 Elsevier Inc. All rights reserved.

关键词： Paramyxovirus assembly Sendai virus Matrix protein structure-function Integrated suppression complementation system

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Unconventional production strategies, action mechanisms, and structure-functional attributes of food-derived peptides

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FOOD HYDROCOLLOIDS 2023年第1期144卷

作者： Le, Thanh-Do Suttikhana, Itthanan Ashaolu, Tolulope Joshua Duy Tan Univ Inst Global Hlth Innovat Da Nang 550000 Vietnam Duy Tan Univ Fac Med Da Nang 550000 Vietnam Univ South Bohemia Fac Agr & Technol Dept Multifunct Agr Ceske Budejovice Czech Republic

Food-derived peptides (FDPs) are constantly increasing in popularity due to their health-promoting potential. However, using the lens of conventional techniques to study FDPs is cumbersome, costly, and slow, leading to the development of novel unconventional or bioinformatic approaches. These methods aid in the rapid and timely prediction of FDPs formation from the available protein data banks, and the analysis of the structure-activity relationships of the peptides. Based on their high efficiency and unique properties of FDPs, they have a wide range of applications. Therefore, this review discussed the most recent developments in non-conventional production strategies of FDPs, especially by using in silico approaches. This is followed by presenting the multifarious factors that affect action mechanisms and structure-function of FDPs with antimicrobial, antioxidant, immunomodulatory, and thermal hysteresis functions. This review's main goal is to provide a much better comprehension of FDPs and prospects that would be acquired to produce next-generation FDPs incorporable into the development of functional foods and nutraceuticals.

关键词： Food-derived peptides Action mechanism structure-function In silico Bioinformatics

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Co-delivery of astaxanthin using positive synergistic effect from biomaterials: From structural design to functional regulation

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FOOD CHEMISTRY 2025年 470卷 142731页

作者： Wang, Fengqiujie Zeng, Jianhua Lin, Liu Wang, Xichang Zhang, Long Tao, Ningping Shanghai Ocean Univ Coll Food Sci & Technol Shanghai Peoples R China Ocean Univ China Coll Food Sci & Engn Qingdao Peoples R China Shanghai Engn Res Ctr Aquat Prod Proc & Preservat Shanghai Peoples R China Shanghai Ocean Univ Natl Expt Teaching Demonstrat Ctr Food Sci & Engn Shanghai Peoples R China

The powerful antioxidant properties of astaxanthin (AST) face two significant challenges: low water solubility and poor chemical stability. To overcome them, extensive research and development efforts have been directed toward creating effective delivery systems. Among them, the positive synergistic effect between biomaterials can be used to refine the design of delivery systems. Understanding the relationship between structure and function aids in tailoring applications to specific needs. This review outlines the challenges associated with delivering AST and reviews the mechanisms involved in creating delivery systems, specifically focusing on the structure-function relationship of biomaterials. It comprehensively introduces the positive synergistic effect of biomaterials with enhancing the functional properties of AST, and analyzes the impact of designed structures on function regulation and the application prospects of the delivery system in the food industry. The future demand for efficient delivery of AST will increasingly depend on the positive synergistic effect between biomaterials.

关键词： Astaxanthin Biomaterials Positive synergistic effect structure-function Food application

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Histone N-tails modulate sequence-specific positioning of nucleosomes

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JOURNAL OF BIOLOGICAL CHEMISTRY 2025年第2期301卷 108138页

作者： Nikitina, Tatiana Guiblet, Wilfried M. Cui, Feng Zhurkin, Victor B. NCI NIH Bethesda MD 20892 USA Rochester Inst Technol Thomas H Gosnell Sch Life Sci Rochester NY 14623 USA Frederick Natl Lab Canc Res Adv Biomed Computat Sci Frederick MD 21701 USA

Spatial organization of chromatin is essential for cellular functioning. However, the precise mechanisms governing sequence-dependent positioning of nucleosomes on DNA remain unknown in detail. Existing algorithms, considering the sequence-dependent deformability of DNA and its interactions with the histone globular domains, predict rotational setting of only 65% of human nucleosomes mapped in vivo. To uncover additional factors responsible for the nucleosome positioning, we analyzed potential involvement of the histone N-tails in this process. To this aim, we reconstituted the H2A/H4 N-tailless nucleosomes on human BRCA1 DNA (100 kb) and compared their positions and sequences with those of the wild-type nucleosomes. We found that removal of the histone N-tails promoted displacement of the predominant positions of nucleosomes, accompanied by redistribution of the AT-rich and GC-rich motifs in nucleosome sequences. Importantly, most of these sequence changes occurred at superhelical locations (SHLs) +/- 4, +/- 1, and +/- 2, where the H2A and H4 N-tails interact with the DNA minor grooves. Furthermore, a substantial number of H4-tailless nucleosomes exhibit rotational settings opposite to that of the wild-type nucleosomes, the effect known to change the topological properties of chromatin fiber. Thus, the histone N-tails are operative in the selection of nucleosome positions, which may have wide-ranging implications for epigenetic modulation of chromatin states.

关键词： nucleosome epigenetics histone modification DNA sequencing DNA structure DNA endonuclease electrostatics structure-function

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The structural basis of substrate selectivity of the acinetobactin biosynthetic adenylation domain, BasE

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JOURNAL OF BIOLOGICAL CHEMISTRY 2025年第4期301卷 108413页

作者： Ahmed, Syed Fardin Gulick, Andrew M. SUNY Buffalo Dept Struct Biol Buffalo NY 14203 USA

Siderophores are small molecule natural products that are often produced by enzymes called nonribosomal peptide synthetases that many pathogenic bacteria produce to adapt to low iron conditions. Nonribosomal peptide synthetase bioengineering could lead to the production of siderophore analogs with the potential to interrupt this unique bacterial iron uptake system, endowing the molecules with antimicrobial properties. Acinetobacter baumannii produces the catecholate siderophore acinetobactin to scavenge iron, a nutrient essential for several metabolic processes. Previous studies have reported synthetic analogs of acinetobactin that disrupt iron acquisition by A. baumannii, resulting in inhibition of bacterial growth. To foster a long-term goal of using a chemoenzymatic approach to produce additional analogs, we have targeted the adenylation domain BasE for the incorporation of alternate substrates. Here, we report a structure-guided approach to investigate the substrate selectivity of BasE for non-native aryl substrates. Using targeted mutagenesis in the active site of BasE, we generated mutants that catalyze the activation of alternate substrates with catalytic efficiencies comparable to the WT enzyme with its natural substrate 2,3-dihydroxybenzoic acid. We further solved structures of these mutants bound to the non-native substrates that illustrate an expanded binding pocket that support the improved promiscuity of BasE. Motivated to develop an approach to produce analogs of acinetobactin, including molecules that could block iron uptake or be readily conjugated to antibiotic cargo, our work aims to develop a structure-guided approach for using catecholate siderophore pathways to incorporate alternate substrates.

关键词： enzyme structure natural product biosynthesis siderophore structural biology structure-function nonribosomal peptide synthetase

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Structural and functional characterization of the extended-diKH domain from the antiviral endoribonuclease KHNYN

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JOURNAL OF BIOLOGICAL CHEMISTRY 2025年第4期301卷 108336页

作者： Youle, Rebecca L. Lista, Maria Jose Bouton, Clement Kunzelmann, Simone Wilson, Harry Cottee, Matthew A. Purkiss, Andrew G. Morris, Elizabeth R. Neil, Stuart J. D. Taylor, Ian A. Swanson, Chad M. Kings Coll London Dept Infect Dis London England Francis Crick Inst Macromol Struct Lab London England Francis Crick Inst Struct Biol Sci Technol Platform London England AstraZeneca Discovery Ctr 1 Francis Crick Ave Cambridge CB2 0AA England Univ Durham Dept Biosci Durham DH1 3LE England

Zinc finger antiviral protein (ZAP) binds CpG dinucleotides in viral RNA and targets them for decay. ZAP interacts with several cofactors to form the ZAP antiviral system, including KHNYN, a multidomain endoribonuclease required for ZAPmediated RNA decay. However, it is unclear how the individual domains in KHNYN contribute to its activity. Here, we demonstrate that the KHNYN amino-terminal extended-diKH (ex-diKH) domain is required for antiviral activity and present its crystal structure. The structure belongs to a rare group of KH-containing domains, characterized by a noncanonical arrangement between two type 1 KH modules, with an additional helical bundle. N4BP1 is a KHNYN paralog with an ex-diKH domain that functionally complements the KHNYN ex-diKH domain. Interestingly, the ex-diKH domain structure is present in N4BP1-like proteins in lancelets, which are basal chordates, indicating that it is evolutionarily ancient. While many KH domains demonstrate RNA binding activity, biolayer interferometry and electrophoretic mobility shift assays indicate that the KHNYN ex-diKH domain does not bind RNA. Furthermore, residues required for canonical KH domains to bind RNA are not required for KHNYN antiviral activity. By contrast, an inter-KH domain cleft in KHNYN is a potential protein-protein interaction site, and mutations that eliminate arginine salt bridges at the edge of this cleft decrease KHNYN antiviral activity. This suggests that this domain could be a binding site for an unknown KHNYN cofactor.

关键词： innate immunity viral replication RNA turnover RNA virus structure-function KHNYN ZAP ZC3HAV1 HIV CpG

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