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The structure-function relationship of a signaling-competent, dimeric Reelin fragment

structure 2021年第10期29卷 1156-+页

作者： Turk, Liam S. Kuang, Xuyuan Dal Pozzo, Valentina Patel, Khush Chen, Muyuan Huynh, Kevin Currie, Michael J. Mitchell, Daniel Dobson, Renwick C. J. D'Arcangelo, Gabriella Dai, Wei Comoletti, Davide Child Hlth Inst New Jersey New Brunswick NJ 08901 USA Rutgers State Univ Robert Wood Johnson Med Sch Dept Neurosci & Cell Biol New Brunswick NJ 08901 USA Victoria Univ Wellington Sch Biol Sci Wellington 6012 New Zealand Rutgers State Univ Dept Cell Biol & Neurosci Piscataway NJ 08854 USA Rutgers State Univ Inst Quantitat Biomed Piscataway NJ 08854 USA Cent South Univ Dept Hyperbar Oxygen Changsha Hunan Peoples R China Baylor Coll Med Verna & Marrs McLean Dept Biochem & Mol Biol Houston TX 77030 USA Univ Canterbury Biomol Interact Ctr Christchurch 8041 New Zealand Univ Canterbury Sch Biol Sci Christchurch 8041 New Zealand Univ Melbourne Dept Biochem & Mol Biol Bio21 Mol Sci & Biotechnol Inst Parkville Vic 3010 Australia

Reelin operates through canonical and non-canonical pathways that mediate several aspects of brain development and function. Reelin's dimeric central fragment (CF), generated through proteolytic cleavage, is required for the lipoprotein-receptor-dependent canonical pathway activation. Here, we analyze the signaling properties of a variety of Reelin fragments and measure the differential binding affinities of monomeric and dimeric CF fragments to lipoprotein receptors to investigate the mode of canonical signal activation. We also present the cryoelectron tomography-solved dimeric structure of Reelin CF and support it using several other biophysical techniques. Our findings suggest that Reelin CF forms a covalent parallel dimer with some degree of flexibility between the two protein chains. As a result of this conformation, Reelin binds to lipoprotein receptors in a manner inaccessible to its monomeric form and is capable of stimulating canonical pathway signaling.

关键词： structure-function Reelin dimer ApoER2 VLDLR cryo-ET SAXS AUC high-content analysis

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Gradients of structure-function tethering across neocortex

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2019年第42期116卷 21219-21227页

作者： Vazquez-Rodriguez, Bertha Suarez, Laura E. Markello, Ross D. Shafiei, Golia Paquola, Casey Hagmann, Patric van den Heuvel, Martijn P. Bernhardt, Boris C. Spreng, R. Nathan Misic, Bratislav McGill Univ Montreal Neurol Inst McConnell Brain Imaging Ctr Montreal PQ H3A 2B4 Canada Ecole Polytech Fed Lausanne Signal Proc Lab LTS5 CH-1015 Lausanne Switzerland Vrije Univ Amsterdam Ctr Neurogen & Cognit Res NL-1081 HV Amsterdam Netherlands

The white matter architecture of the brain imparts a distinct signature on neuronal coactivation patterns. Interregional projections promote synchrony among distant neuronal populations, giving rise to richly patterned functional networks. A variety of statistical, communication, and biophysical models have been proposed to study the relationship between brain structure and function, but the link is not yet known. In the present report we seek to relate the structural and functional connection profiles of individual brain areas. We apply a simple multilinear model that incorporates information about spatial proximity, routing, and diffusion between brain regions to predict their functional connectivity. We find that structure-function relationships vary markedly across the neocortex. structure and function correspond closely in unimodal, primary sensory, and motor regions, but diverge in transmodal cortex, particularly the default mode and salience networks. The divergence between structure and function systematically follows functional and cytoarchitectonic hierarchies. Altogether, the present results demonstrate that structural and functional networks do not align uniformly across the brain, but gradually uncouple in higher-order polysensory areas.

关键词： connectome structure-function cortical gradient

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Recent advances in the structure, function and regulation of the volume-regulated anion channels and their role in immunity

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JOURNAL OF PHYSIOLOGY-LONDON 2024年第0期 2024 Dec 22页

作者： Yanushkevich, Sergei Zieminska, Aleksandra Gonzalez, Joshua Anazco, Francisca Song, Richard Arias-Cavieres, Alejandra Granados, Sara T. Zou, Junyi Rao, Yan Concepcion, Axel R. Univ Chicago Dept Biochem & Mol Biol 929 East 57th StGCIS West Bldg Chicago IL 60637 USA Univ Chicago Comm Immunol Chicago IL USA Univ Chicago Inst Biophys Dynam Chicago IL USA Univ Chicago Med Comprehens Canc Ctr Chicago IL USA

Volume-regulated anion channels (VRACs) are heteromeric complexes formed by proteins of the leucine-rich repeat-containing 8 (LRRC8) family. LRRC8A (also known as SWELL1) is the core subunit required for VRAC function, and it must combine with one or more of the other paralogues (i.e. LRRC8B-E) to form functional heteromeric channels. VRACs were discovered in T lymphocytes over 35 years ago and are found in virtually all vertebrate cells. Initially, these anion channels were characterized for their role in Cl- efflux during the regulatory volume decrease process triggered when cells are subjected to hypotonic challenges. However, substantial evidence suggests that VRACs also transport small molecules under isotonic conditions. These findings have expanded the research on VRACs to explore their functions beyond volume regulation. In innate immune cells, VRACs promote inflammation by modulating the transport of immunomodulatory cyclic dinucleotides, itaconate and ATP. In adaptive immune cells, VRACs suppress their function by taking up cyclic dinucleotides to activate the STING signalling pathway. In this review, we summarize the current understanding of LRRC8 proteins in immunity and discuss recent progress in their structure, function, regulation and mechanisms for channel activation and gating. Finally, we also examine potential immunotherapeutic applications of VRAC modulation. image

关键词： immunotherapy LRRC8 macrophages structure-function T cells VRAC

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Ce-modified mesoporous γ-Al2O3 supported Pd-Pt nanoparticle catalysts and their structure-function relationship in complete benzene oxidation

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CHEMICAL ENGINEERING JOURNAL 2019年 356卷 255-261页

作者： Chen, Zhu Li, Jing Yang, Peng Cheng, Zhen Li, Jingrong Zuo, Shufeng Shaoxing Univ Zhejiang Key Lab Alternat Technol Fine Chem Proc Shaoxing 312000 Peoples R China Liaocheng Univ Coll Chem & Chem Engn Shandong Prov Key Lab Chem Energy Storage & Novel Liaocheng 252059 Peoples R China

In this investigation, a mesoporous gamma-Al2O3 with large surface area and good thermal stability was synthesized and employed as the support for preparing a series of Pd-Pt nanocrystalline catalysts by using a high-temperature solution-phase reduction method. The PdOx (x = 0, 1) and PtOx (x = 0, 2) nanoparticles were found to have a small diameter(about 2 nm) and were highly dispersed on the surface of the mesoporous gamma-Al2O3. The results show that catalysts with the appropriate ceria greatly improved the physical adsorption/chemisorption of benzene to Pd-Pt nanocrystals, which greatly enhanced the activity to achieve the complete oxidation of benzene. The high activity of the catalyst was mainly due to the nano-effects of Pd-Pt nanocrystals and the interactions among the active components. 0.2% Pd-Pt(1:1)/10% Ce/gamma-Al2O3 demonstrated the best activity for the complete oxidation of benzene at 200 degrees C. Furthermore, this catalyst maintained 95% benzene conversion for 1000 h at 190 degrees C and displayed good resistance to water and Cl-poisoning, which indicated that the Pd-Pt nanocrystalline catalysts have promise for adoption by the industry.

关键词： Pd-Pt nanocrystals Nano-effects structure-function VOC Catalytic oxidation

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Game-based activities targeting visual literacy skills to increase understanding of biomolecule structure and function concepts in undergraduate biochemistry

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BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION 2021年第1期49卷 94-107页

作者： Terrell, Cassidy R. Nickodem, Kyle Bates, Alison Kersten, Cassandra Mernitz, Heather Univ Minnesota Ctr Learning Innovat 111 S Broadway Rochester MN 55904 USA Univ Minnesota Dept Educ Psychol Quantitat Methods Educ Minneapolis MN USA Alverno Coll Dept Phys Sci Milwaukee WI USA

Introductory biochemistry courses are often challenging for students because they require the integration of chemistry, biology, physics, math, and physiology knowledge and frameworks to understand and apply a large body of knowledge. This can be complicated by students' persistent misconceptions of fundamental concepts and lack of fluency with the extensive visual and symbolic literacy used in biochemistry. Card sorting tasks and game-based activities have been used to reveal insights into how students are assimilating, organizing, and structuring disciplinary knowledge, and how they are progressing along a continuum from disciplinary novice to expert. In this study, game-based activities and card sorting tasks were used to promote and evaluate students' understanding of fundamental structure-function relationships in biochemistry. Our results suggest that while many markers of expertise increased for both the control and intervention groups over the course of the semester, students involved in the intervention activities tended to move further towards expert-like sorting. This indicates that intentional visual literacy game-based activities have the ability to build underdeveloped skills in undergraduate students.

关键词： active learning biochemistry biomolecules card sorting game-based novice expert structure-function visual literacy

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Synthesis, in vitro and cellular antioxidant activity evaluation of novel peptides derived from Saccharomyces cerevisiae protein hydrolysate: structure-function relationship Antioxidant activity and synthetic peptides

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AMINO ACIDS 2019年第8期51卷 1167-1175页

作者： Mirzaei, Mahta Mirdamadi, Saeed Safavi, Maliheh Zare, Davood Hadizadeh, Mahnaz Asadi, Mahnaz Mazaheri Islamic Azad Univ Shahr E Qods Branch Dept Food Sci & Technol Tehran Iran IROST Dept Biotechnol Tehran Iran

The relationship between structure and function of primary antioxidant peptide, YR-10 (YGKPVAVPAR) was considered by synthesizing three analogues including YHR-10 (YGKHVAVHAR), GA-8 (GKPVAVPA) and PAR-3 (PAR). Antioxidant activity was determined through in vitro and cellular assays. Substitution of Pro with His in the structure of YR-10 led to significant (P < 0.05) higher ABTS radical scavenging and ferric reducing activity. Following in silico simulated gastrointestinal digestion, Tyr and Arg were omitted, respectively, from N and C-terminal positions and resulted in decreasing DPPH, ABTS radical scavenging, and ferric reducing activities. PAR-3 showed the best inhibitory activity on linoleic acid oxidation. Pretreatment of Caco-2 cells with YR-10, YHR-10, and GA-8 (1000 mu M) before exposure to H2O2 (160 mu M) resulted in 34.10%, 39.66% and 29.159% reduction in malondialdehyde and 53.52%, 17.02% and 24.71% reduction in protein carbonyl levels. The peptide pretreatment reduced catalase level in cells and PAR-3 exhibited the most protective effects on the viability of cells exposed to oxidative stress.

关键词： Synthetic peptides structure-function Antioxidant activity Caco-2 cells

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Chemical Modification of Acidic Residues of Cytochrome c with Safranin: pH Effect on structure and function of the Modified Protein

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CHEMISTRYSELECT 2023年第1期8卷

作者： Hashemnia, Sedigheh Karmand, Zahra Mokhtari, Zaynab Persian Gulf Univ Fac Nano & Bio Sci & Technol Dept Chem Bushehr 75169 Iran Tech & Vocat Univ TVU Dept Chem Ind Bushehr Iran

Utilizing cytochrome c (Cyt c), we studied the covalent attachment of safranin O to a protein could affect the protein properties. The effect of covalent attachment of safranin to Cyt c was explored using spectroscopic techniques, which revealed changes in the secondary and tertiary structure of the protein. Using Trp 59 fluorescence emission (lambda(em)=355 nm) and safranin fluorescence profile (lambda(em)=587 nm), we investigated the changes in the structure of the heme moiety and the binding of safranin molecules to the Cyt c protein. Far-UV CD spectroscopy results showed that modification significantly reduced the alpha-helix content. Studies showed that the modification causes the prevention of thermal aggregation of the protein at 65 degrees C and decreases in the peroxidase activity of the protein. Investigating of the pH effect revealed that although the Cyt c modification reduced peroxidase activity, the pH shift to pH 6.0 could increase the peroxidase activity.

关键词： Chemical modification Cytochrome c Peroxidase activity Safranin O structure-function

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The molecular mechanism of SLC34 proteins: insights from two decades of transport assays and structure-function studies

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PFLUGERS ARCHIV-EUROPEAN JOURNAL OF PHYSIOLOGY 2019年第1期471卷 15-42页

作者： Forster, Ian C. Florey Inst Neurosci & Mental Hlth Ion Channels & Human Dis Lab 30 Royal Parade Parkville Vic 3052 Australia

The expression cloning some 25years ago of the first member of SLC34 solute carrier family, the renal sodium-coupled inorganic phosphate cotransporter (NaPi-IIa) from rat and human tissue, heralded a new era of research into renal phosphate handling by focussing on the carrier proteins that mediate phosphate transport. The cloning of NaPi-IIa was followed by that of the intestinal NaPi-IIb and renal NaPi-IIc isoforms. These three proteins constitute the main secondary-active Na+-driven pathways for apical entry of inorganic phosphate (P-i) across renal and intestinal epithelial, as well as other epithelial-like organs. The key role these proteins play in mammalian P-i homeostasis was revealed in the intervening decades by numerous in vitro and animal studies, including the development of knockout animals for each gene and the detection of naturally occurring mutations that can lead to P-i-handling dysfunction in humans. In addition to characterising their physiological regulation, research has also focused on understanding the underlying transport mechanism and identifying structure-function relationships. Over the past two decades, this research effort has used real-time electrophysiological and fluorometric assays together with novel computational biology strategies to develop a detailed, but still incomplete, understanding of the transport mechanism of SLC34 proteins at the molecular level. This review will focus on how our present understanding of their molecular mechanism has evolved in this period by highlighting the key experimental findings.

关键词： Phosphate cotransport Electrophysiology Fluorometry Kinetics structure-function

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structure-function relationship exploration for enhanced electro-optic activity in isophorone-based organic NLO chromophores

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DYES AND PIGMENTS 2018年 157卷 55-63页

作者： Liu, Fenggang Zhang, Hua Xiao, Hongyan Xu, Huajun Bo, Shuhui Qiu, Ling Zhen, Zhen Lai, Lijie Chen, Shujie Wang, Jiahai Guangzhou Univ Guangzhou Key Lab Environm Funct Mat & Technol Sch Chem & Chem Engn Guangzhou 510006 Guangdong Peoples R China Chinese Acad Sci Tech Inst Phys & Chem Key Lab Photochem Convers & Optoelect Mat Beijing 100190 Peoples R China

Four isophorone-based chromophores FLD1-FLD4 has been synthesized and investigated based on julolidinyl donors, with modified isophorone-derived bridges and tricyanovinyl-dihydrofuran or phenyl-trifluoromethyltricyanofuran acceptors. The chromophore FLD3 was modified with a 2-((tert-butyldimethylsilyl)oxy)ethanethiol group covalently attached to the pi-conjugate bridge to ensure its all-trans conformation and prevent close packing of molecules, which benefit the macroscopic electro-optic efficiency. The chromophore FLD3 possesses better thermal stability than chromophore FLD1 without the isolation group on the bridge. Moreover, density functional theory calculations suggested that the hyperpolarizability (beta) value of chromophore FLD3 is larger than that of chromophore FLD1. Polymers doped with chromophore FLD3 have been poled to afford ultrahigh electro-optic coefficient (r(33)) of 238 pm/V at 1.31 pm, which is nearly 60% higher than that obtained from chromophore FLD1 and three times higher than that of analogue chromophores FLD2 and FLD4.

关键词： Nonlinear optics Chromophore Isolation group Electro-optic Isophorone structure-function

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structure and function of a flavin-dependent S-monooxygenase from garlic (Allium sativum)

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JOURNAL OF BIOLOGICAL CHEMISTRY 2020年第32期295卷 11042-11055页

作者： Valentino, Hannah Campbell, Ashley C. Schuermann, Jonathan P. Sultana, Nazneen Nam, Han G. LeBlanc, Sophie Tanner, John J. Sobrado, Pablo Virginia Tech Dept Biochem Blacksburg VA 24061 USA Virginia Tech Ctr Drug Discovery Blacksburg VA 24061 USA Univ Missouri Dept Biochem Columbia MO 65201 USA Cornell Univ Northeastern Collaborat Access Team Dept Chem & Chem Biol Ithaca NY USA Univ Missouri Dept Chem Columbia MO 65211 USA

Allicin is a component of the characteristic smell and flavor of garlic (Allium sativum). A flavin-containing monooxygenase (FMO) produced byA. sativum(AsFMO) was previously proposed to oxidizeS-allyl-l-cysteine (SAC) to alliin, an allicin precursor. Here, we present a kinetic and structural characterization of AsFMO that suggests a possible contradiction to this proposal. Results of steady-state kinetic analyses revealed that AsFMO exhibited negligible activity with SAC;however, the enzyme was highly active withl-cysteine,N-acetyl-l-cysteine, and allyl mercaptan. We found that allyl mercaptan with NADPH was the preferred substrate-cofactor combination. Rapid-reaction kinetic analyses showed that NADPH binds tightly (K(D)of similar to 2 mu m) to AsFMO and that the hydride transfer occurs with pro-Rstereospecificity. We detected the formation of a long-wavelength band when AsFMO was reduced by NADPH, probably representing the formation of a charge-transfer complex. In the absence of substrate, the reduced enzyme, in complex with NADP(+), reacted with oxygen and formed an intermediate with a spectrum characteristic of C4a-hydroperoxyflavin, which decays several orders of magnitude more slowly than thek(cat). The presence of substrate enhanced C4a-hydroperoxyflavin formation and, upon hydroxylation, oxidation occurred with a rate constant similar to thek(cat). The structure of AsFMO complexed with FAD at 2.08-angstrom resolution features two domains for binding of FAD and NADPH, representative of class B flavin monooxygenases. These biochemical and structural results are consistent with AsFMO being an S-monooxygenase involved in allicin biosynthesis through direct formation of sulfenic acid and not SAC oxidation.

关键词： flavin-dependent monooxygenases sulfenic acid S-oxygenation allicin class B monooxygenases allyl mercaptan hydroxylation garlic (Allium sativum) natural product biosynthesis structure-function flavin FAD natural product plant biochemistry oxidation-reduction (redox) C4a-hydroperoxyflavin

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