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1.
    
Bacterial microcompartment (MCP) organelles are cytosolic, polyhedral structures consisting of a thin protein shell and a series of encapsulated, sequentially acting enzymes. To date, different microcompartments carrying out three distinct types of metabolic processes have been characterized experimentally in various bacteria. In the present work, we use comparative genomics to explore the existence of yet uncharacterized microcompartments encapsulating a broader set of metabolic pathways. A clustering approach was used to group together enzymes that show a strong tendency to be encoded in chromosomal proximity to each other while also being near genes for microcompartment shell proteins. The results uncover new types of putative microcompartments, including one that appears to encapsulate B12‐independent, glycyl radical‐based degradation of 1,2‐propanediol, and another potentially involved in amino alcohol metabolism in mycobacteria. Preliminary experiments show that an unusual shell protein encoded within the glycyl radical‐based microcompartment binds an iron‐sulfur cluster, hinting at complex mechanisms in this uncharacterized system. In addition, an examination of the computed microcompartment clusters suggests the existence of specific functional variations within certain types of MCPs, including the alpha carboxysome and the glycyl radical‐based microcompartment. The findings lead to a deeper understanding of bacterial microcompartments and the pathways they sequester.  相似文献   

2.
    
Carboxysomes are primitive bacterial organelles that function as a part of a carbon concentrating mechanism (CCM) under conditions where inorganic carbon is limiting. The carboxysome enhances the efficiency of cellular carbon fixation by encapsulating together carbonic anhydrase and the CO2-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). The carboxysome has a roughly icosahedral shape with an outer shell between 800 and 1500 Å in diameter, which is constructed from a few thousand small protein subunits. In the cyanobacterium Synechocystis sp. PCC 6803, the previous structure determination of two homologous shell protein subunits, CcmK2 and CcmK4, elucidated how the outer shell is formed by the tight packing of CcmK hexamers into a molecular layer. Here we describe the crystal structure of the hexameric shell protein CcmK1, along with structures of mutants of both CcmK1 and CcmK2 lacking their sometimes flexible C-terminal tails. Variations in the way hexamers pack into layers are noted, while sulfate ions bound in pores through the layer provide further support for the hypothesis that the pores serve for transport of substrates and products into and out of the carboxysome. One of the new structures provides a high-resolution (1.3 Å) framework for subsequent computational studies of molecular transport through the pores. Crystal and solution studies of the C-terminal deletion mutants demonstrate the tendency of the terminal segments to participate in protein—protein interactions, thereby providing a clue as to which side of the molecular layer of hexameric shell proteins is likely to face toward the carboxysome interior.  相似文献   

3.
    
Coassembled peptide amphiphile nanofibers designed to target atherosclerotic plaque and enhance cholesterol efflux are shown to encapsulate and deliver a liver X receptor agonist to increase efflux from murine macrophages in vitro. Fluorescence microscopy reveals that the nanofibers, which display an apolipoprotein‐mimetic peptide, localize at plaque sites in low density lipoprotein receptor knockout (LDLR KO) mice with or without the encapsulated molecule, while nanofibers displaying a scrambled, nontargeting peptide sequence do not demonstrate comparable binding. These results show that nanofibers functionalized with apolipoprotein‐mimetic peptides may be effective vehicles for intravascular targeted drug delivery to treat atherosclerosis.  相似文献   

4.
    
Circular dichroism (CD) spectroscopy has been used extensively for the investigation of the conformation and configuration of chiral molecules, but its use for evaluating the mode of self‐assembly in soft materials has been limited. Herein, we report a protocol for the study of such materials by electronic CD spectroscopy using commercial/benchtop instruments and synchrotron radiation (SR) using the B23 beamline available at Diamond Light Source. The use of the B23 beamtime for SRCD was advantageous because of the unique enhanced spatial resolution achieved because of its highly collimated and small beamlight cross section (ca. 250 μm) and higher photon flux in the far UV region (175‐250 nm) enhancing the signal‐to‐noise ratio relative to benchtop CD instruments. A set of low molecular weight (LMW) hydrogelators, comprising two Fmoc‐protected enantiomeric monosaccharides and one Fmoc dipeptide (Fmoc‐FF), were studied. The research focused on the optimization of sample preparation and handling, which then enabled the characterization of sample conformational homogeneity and thermal stability. CD spectroscopy, in combination with other spectroscopic techniques and microscopy, will allow a better insight into the self‐assembly of chiral building blocks into higher order structural architectures.  相似文献   

5.
Per-O-methylated β-cyclodextrin (CD) bearing an iodoacetamide group at the 6-position was synthesized to functionalize protein surfaces. Bovine serum albumin (BSA) was quantitatively modified with the CD derivative by the S(N) 2 reaction of iodoacetamide with a cysteine residue (Cys34) on the BSA surface. The resultant CD-functionalized BSA (BSA-CD) spontaneously dimerized upon addition of an anionic tetraarylporphyrin (TPPS) through the supramolecular 1:2 complexation between TPPS and CD on the protein surface. The BSA-CD/TPPS complex further complexed with ferric protoporphyrin IX (hemin) in the hydrophobic pockets of albumin to form a hemin/BSA-CD/TPPS ternary complex in which static fluorescence quenching occurred owing to intramolecular electron transfer from the photoexcited TPPS to hemin.  相似文献   

6.
    
The use of stereodynamic probes is becoming one of the leading strategies for the fast and effective determination of enantiomeric excess. Recently, we reported a series of novel molecular architectures based on a modified tris(2‐pyridylmethyl)amine complex (TPMA), which are able to amplify the electronic CD, in the case of Zn(II) assemblies and vibrational CD, in the case of Co(II) assemblies. Herein, we report a structural modification of the ligand with the purpose to obtain a fluorescent chiral probe. The study deals with the synthesis of the novel ligand, the formation of the self‐assembly system with amino acids, and the study of the electronic CD and circularly polarized luminescence.  相似文献   

7.
    
Bacterial microcompartments (MCPs) are subcellular organelles that are composed of a protein shell and encapsulated metabolic enzymes. It has been suggested that MCPs can be engineered to encapsulate protein cargo for use as in vivo nanobioreactors or carriers for drug delivery. Understanding the stability of the MCP shell is critical for such applications. Here, we investigate the integrity of the propanediol utilization (Pdu) MCP shell of Salmonella enterica over time, in buffers with various pH, and at elevated temperatures. The results show that MCPs are remarkably stable. When stored at 4°C or at room temperature, Pdu MCPs retain their structure for several days, both in vivo and in vitro. Furthermore, Pdu MCPs can tolerate temperatures up to 60°C without apparent structural degradation. MCPs are, however, sensitive to pH and require conditions between pH 6 and pH 10. In nonoptimal conditions, MCPs form aggregates. However, within the aggregated protein mass, MCPs often retain their polyhedral outlines. These results show that MCPs are highly robust, making them suitable for a wide range of applications.  相似文献   

8.
    
A novel porphyrin‐C60 dyad (PCD1) is designed and synthesized to investigate and manipulate the supramolecular structure where geometrically isotropic [such as [60]fullerene (C60)] and anisotropic [such as porphyrin (Por)] units coexist. It is observed that PCD1 possesses an enantiomeric phase behavior. The melting temperature of the stable PCD1 thermotropic phase is 160 °C with a latent heat (ΔH) of 18.5 kJ mol?1. The phase formation is majorly driven by the cooperative intermolecular Por–Por and C60–C60 interactions. Structural analysis reveals that this stable phase possesses a supramolecular “double‐cable” structure with one p‐type Por core columnar channel and three helical n‐type C60 peripheral channels. These “double‐cable” columns further pack into a hexagonal lattice with a = b = 4.65 nm, c = 41.3 nm, α = β = 90°, and γ = 120°. The column repeat unit is determined to possess a 12944 helix. With both donor (D; Pro) and acceptor (A; C60) units having their own connecting channels as well as the large D/A interface within the supramolecular “double‐cable” structure, PCD1 has photogenerated carriers with longer lifetimes compared to the conventional electron acceptor [6,6]‐phenyl‐C61‐butyric acid methyl ester. A phase‐separated columnar morphology is observed in a bulk‐heterojunction (BHJ) material made by the physical blend of a low band‐gap conjugated polymer, [poly[2,6‐(4,4‐bis‐(2‐ethylhexyl)‐4H‐cyclopenta [2,1‐b;3,4‐b′]‐dithiophene)‐alt‐4,7‐(2,1,3‐benzothia‐diazole)] (PCPDTBT), and PCD1. With a specific phase structure in the solid state and in the blend, PCD1 is shown to be a promising candidate as a new electron acceptor in high performance BHJ polymer solar cells.  相似文献   

9.
    
Coiled coil is a ubiquitous structural motif in proteins, with two to seven alpha helices coiled together like the strands of a rope, and coiled coil folding and assembly is not completely understood. A GCN4 leucine zipper mutant with four mutations of K3A, D7A, Y17W, and H18N has been designed, and the crystal structure has been determined at 1.6 Å resolution. The peptide monomer shows a helix trunk with short curved N‐ and C‐termini. In the crystal, two monomers cross in 35° and form an X‐shaped dimer, and each X‐shaped dimer is welded into the next one through sticky hydrophobic ends, thus forming an extended two‐stranded, parallel, super long coiled coil rather than a discrete, two‐helix coiled coil of the wild‐type GCN4 leucine zipper. Leucine residues appear at every seventh position in the super long coiled coil, suggesting that it is an extended super leucine zipper. Compared to the wild‐type leucine zipper, the N‐terminus of the mutant has a dramatic conformational change and the C‐terminus has one more residue Glu 32 determined. The mutant X‐shaped dimer has a large crossing angle of 35° instead of 18° in the wild‐type dimer. The results show a novel assembly mode and oligomeric state of coiled coil, and demonstrate that mutations may affect folding and assembly of the overall coiled coil. Analysis of the formation mechanism of the super long coiled coil may help understand and design self‐assembling protein fibers.  相似文献   

10.
    
A hemoprotein‐based supramolecular polymer that has a covalently linked heme moiety on the protein surface has been constructed based on interprotein heme–heme pocket interactions of the chemically modified apocytochrome b562 ( 1 ‐H63C). The thermodynamic properties of the polymer have been investigated by means of size exclusion chromatography, UV–vis spectroscopy, and circular dichroism spectroscopy. The results indicate that, as with other synthetic systems reported so far, the 1 ‐H63C hemoprotein assembly is thermodynamically controlled in aqueous solution: the degree of polymerization is dependent on the 1 ‐H63C concentration and is modulated by the addition of the end‐capping units, native heme, and/or apocytochrome b562 mutant (apoH63C). These properties suggest a potential use for the hemoprotein self‐assembly in preparation of stimuli‐responsive functional nanobiomaterials. © 2008 Wiley Periodicals, Inc. Biopolymers 91: 194–200, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com  相似文献   

11.
    
The present work describes the synthesis and characterization of α/γ hybrid peptides, Boc‐Phe‐γ4‐Phe‐Val‐OMe, P1 ; Boc‐Ala‐γ4‐Phe‐Val‐OMe, P2 ; and Boc‐Leu‐γ4‐Phe‐Val‐OMe, P3 together with the formation of self‐assembled structures formed by these hybrid peptides in dimethyl sulfoxide (DMSO)/water (1:1). The self‐assembled structures were characterized by infrared (IR) spectroscopy, circular dichroism (CD), and scanning electron microscopy (SEM). Further, α/γ hybrid peptide self‐assembled structures were evaluated for antibacterial properties. Among all, the self‐assembled peptide P1 exhibited the antimicrobial activity against Escherichia coli and Klebsiella pneumoniae, while self‐assembled peptide P3 inhibited the biofilms of Salmonella typhimurium and Pseudomonas aeruginosa. In this study, we have shown the significance of self‐assembled structures formed from completely hydrophobic α/γ hybrid peptides in exploring the antibacterial properties together with biofilm inhibition.  相似文献   

12.
    
Proteins hold great promise in forming complex nanoscale structures which could be used in the development of new nanomaterials, devices, biosensors, electronics, and pharmaceuticals. The potential to produce nanomaterials from proteins is well supported by the numerous examples of self‐assembling proteins found in nature. We have explored self‐assembling proteins for use as supramolecular building blocks, or tectons, specifically the N‐terminal domain of Lsr2, Nterm‐Lsr2. A key feature of this protein is that it undergoes self‐assembly via proteolytic cleavage, thereby allowing us to generate supramolecular assemblies in response to a specific trigger. Herein, we report the effects of pH and protein concentration on the oligomerization of Nterm‐Lsr2. Furthermore, via protein engineering, we have introduced a new trigger for oligomerization via enteropeptidase cleavage. The new construct of Nterm‐Lsr2 can be activated and assembled in a controlled fashion and provides some ability to alter the ratio of higher ordered structures formed. © 2014 Wiley Periodicals, Inc. Biopolymers 103: 260–270, 2015.  相似文献   

13.
    
Two pyrene based organogelators in which the pyrene moiety has been linked to the diphenylalanine dipeptide have been synthesized. We show how the solvent can tune both the morphology and the optical properties of the organogels: spherical aggregates with quenched emission were obtained in acetonitrile, whereas an entangled fibrillar network with enhanced emission was formed in o‐dichlorobenzene. Fourier transform infrared spectroscopy, circular dichroism and nuclear magnetic resonance spectroscopy experiments suggest that both π–π stacking and hydrogen bonding contribute to the formation of the supramolecular networks. Ultraviolet–visible and steady state emission studies demonstrated the formation of I‐aggregates in acetonitrile. In contrast, in o‐dichlorobenzene, the formation of J‐type aggregates leads to assemblies with enhanced emission. These results give some insight into the important role of the gelling solvent in the morphology of the supramolecular gels and may help in the design of new soft‐materials. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.  相似文献   

14.
    
Bhosale S  Matile S 《Chirality》2006,18(10):849-856
Precise supramolecular architecture is often essential for significant function. Simple methods to reliably and rapidly demonstrate the existence of such supramolecular structure and function at relevant concentrations in complex systems are badly needed. Hill plots, describing the dependence of a signal on the n-th power of the monomer concentration, are compatible only with the identification of supramolecules that do not really exist, that is, endergonic self-assembly (Litvinchuk et al., J Am Chem Soc 2004;126:10067). Here, we show that the artificial increase in monomer concentration by chemical denaturation restores compatibility of Hill plots with exergonic self-assembly and affords Hill coefficients n > 1 for stable supramolecules. Recent rigid-rod pi-stack architecture with photosynthetic and ion channel activity is used as timely example, circular dichroism (CD) spectroscopy as method of choice for both sensitive and selective detection under relevant conditions.  相似文献   

15.
    
Supramolecular systems that respond to the hydrolysis of adenosine phosphates (APs) are attractive for biosensing and to fabricate bioinspired self‐assembled materials. Here, we report on the formation of supramolecular complexes between an achiral guanidinium derivative bearing two pyrene moieties, with each of the three adenosine phosphates: AMP, ADP, and ATP. By combining results from circular dichroism spectroscopy and molecular modeling simulations, we explore the induced chirality, the dynamics of the complexes, and the interactions at play, which altogether provide insights into the supramolecular self‐assembly between APs and the guanidinium‐bispyrene. Finally, we identify the chiroptical signals of interest in mixtures of the guanidinium derivative with the three APs in different proportions. This study constitutes a basis to evolve toward a chiroptical detection of the hydrolysis of APs based on organic supramolecular probes.  相似文献   

16.
    
The ethanolamine utilization (Eut) microcompartment is a protein-based metabolic organelle that is strongly associated with pathogenesis in bacteria that inhabit the human gut. The exterior shell of this elaborate protein complex is composed from a few thousand copies of BMC-domain shell proteins, which form a semi-permeable diffusion barrier that provides the interior enzymes with substrates and cofactors while simultaneously retaining metabolic intermediates. The ability of this protein shell to regulate passage of substrate and cofactor molecules is critical for microcompartment function, but the details of how this diffusion barrier can allow the passage of large cofactors while still retaining small intermediates remain unclear. Previous work has revealed two conformations of the EutL shell protein, providing substantial evidence for a gated pore that might allow the passage of large cofactors. Here we report structural and biophysical evidence to show that ethanolamine, the substrate of the Eut microcompartment, acts as a negative allosteric regulator of EutL pore opening. Specifically, a series of X-ray crystal structures of EutL from Clostridium perfringens, along with equilibrium binding studies, reveal that ethanolamine binds to EutL at a site that exists in the closed-pore conformation and which is incompatible with opening of the large pore for cofactor transport. The allosteric mechanism we propose is consistent with the cofactor requirements of the Eut microcompartment, leading to a new model for EutL function. Furthermore, our results suggest the possibility of redox modulation of the allosteric mechanism, opening potentially new lines of investigation.  相似文献   

17.
    
Sakai N  Matile S 《Chirality》2003,15(9):766-771
Does osmotic pressure stimulate assembly or disassembly of supramolecules in vesicles? Self‐assembly was conceivable as intravesicular response to osmotic shrinking upon application of extravesicular overpressure, whereas disassembly was conceivable as a response to bilayer stress in hyperosmotic vesicles. Self‐assembly of guanosine 5′‐monophosphates (GMPs) into G‐quartets was selected to investigate the nature of remote control of supramolecular chemistry within vesicles by osmotic pressure. Using circular dichroism spectroscopy to selectively detect G‐quartets, we found that extravesicular overpressure stimulates intravesicular self‐assembly, whereas underpressure stimulates disassembly. G‐quartet self‐assembly by osmotic pressure exhibited ion‐selective metal‐cation templation, as expected. The key conclusions are that supramolecular chemistry within vesicles is governed by vesicle shape rather than vesicle stress and that detection of osmotic pressure by CD spectroscopy is an interesting alternative to the commonly used methods based on fluorescence self‐quenching. Chirality 15:766–771, 2003. © 2003 Wiley‐Liss, Inc.  相似文献   

18.
    
Four Ala‐Ala dipeptides with a perfluoroalkyl chain at the N‐terminal were synthesized. They were able to self‐assemble into helical nanofibers and/or twisted nanobelts in a mixture of DMSO/H2O. The handedness of nanofibers and nanobelts was controlled by the chirality of the alanine at the N‐terminal. The stacking handedness of the phenylene groups and the helicity of the perfluoroalkyl chain were studied using circular dichroism spectroscopy and vibrational circular dichroism, respectively. The chirality of the alanine at N‐terminal controlled the stacking handedness of the neighboring phenylene groups. Moreover, due to the low potential barrier between M‐ and P‐helices of the perfluorocarbon chain, the handedness of the organic self‐assemblies eventually controlled the helicity of the perfluorocarbon chain. X‐ray diffraction indicated that a lamellar structure was formed by the dimers of the dipeptides.  相似文献   

19.
Orthology,paralogy and proposed classification for paralog subtypes   总被引：1，自引：0，他引：1  
The paper clears up confusions about the concepts of orthology and paralogy, particularly in cases involving gene family expansions. The terms ‘inparalog’ and ‘outparalog’ are defined to distinguish ancient paralogs from lineage-specific ones.  相似文献   

20.
    
Amelogenin is a proline‐rich enamel matrix protein known to play an important role in the oriented growth of enamel crystals. Amelogenin self‐assembles to form nanospheres and higher order structures mediated by hydrophobic interactions. This study aims to obtain a better insight into the relationship between primary–secondary structure and self‐assembly of amelogenin by applying computational and biophysical methods. Variable temperature circular dichroism studies indicated that under physiological pH recombinant full‐length porcine amelogenin contains unordered structures in equilibrium with polyproline type II (PPII) structure, the latter being more populated at lower temperatures. Increasing the concentration of rP172 resulted in the promotion of folding to an ordered β‐structured assembly. Isothermal titration calorimetry dilution studies revealed that at all temperatures, self‐assembly is entropically driven due to the hydrophobic effect and the molar heat of assembly (ΔHA) decreases with temperature. Using a computational approach, a profile of domains in the amino acid sequence that have a high propensity to assemble and to have PPII structures has been identified. We conclude that the assembly properties of amelogenin are due to complementarity between the hydrophobic and PPII helix prone regions. Proteins 2009. © 2009 Wiley‐Liss, Inc.  相似文献   

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