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KCTD5 is endowed with large, functionally relevant, interdomain motions

JOURNAL OF BIOMOLECULAR structure & DYNAMICS 2016年第8期34卷 1725-1735页

作者： Barone, Daniela Balasco, Nicole Vitagliano, Luigi CNR Inst Biostruct & Bioimaging Via Mezzocannone 16 I-80134 Naples Italy Seconda Univ Napoli Dipartimento Sci & Tecnol Ambientali Biol & Farma I-81100 Caserta Italy

The KCTD family is an emerging class of proteins that are involved in important biological processes whose biochemical and structural properties are rather poorly characterized or even completely undefined. We here used KCTD5, the only member of the family with a known three-dimensional structure, to gain insights into the intrinsic structural stability of the C-terminal domain (CTD) and into the mutual dynamic interplay between the two domains of the protein. Molecular dynamics (MD) simulations indicate that in the simulation timescale (120ns), the pentameric assembly of the CTD is endowed with a significant intrinsic stability. Moreover, MD analyses also led to the identification of exposed -strand residues. Being these regions intrinsically sticky, they could be involved in the substrate recognition. More importantly, simulations conducted on the full-length protein provide interesting information of the relative motions between the BTB domain and the CTD of the protein. Indeed, the dissection of the overall motion of the protein is indicative of a large interdomain twisting associated with limited bending movements. Notably, MD data indicate that the entire interdomain motion is pivoted by a single residue (Ser150) of the hinge region that connects the domains. The functional relevance of these motions was evaluated in the context of the functional macromolecular machinery in which KCTD5 is involved. This analysis indicates that the interdomain twisting motion here characterized may be important for the correct positioning of the substrate to be ubiquitinated with respect to the other factors of the ubiquitination machinery.

关键词： twisting molecular dynamics structure-function relationships substrate recognition domain ubiquitination

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The glycocins: in a class of their own

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CURRENT OPINION IN STRUCTURAL BIOLOGY 2016年 40卷 112-119页

作者： Norris, Gillian E. Patchett, Mark L. Massey Univ Coll Sci Inst Fundamental Sci Private Bag 11222 Palmerston North 4442 New Zealand

First reported in 2011, glycocins (glycosylated bacteriocins) are bacterial toxins that constitute a subset of ribosomally synthesised and post-translationally modified peptide (RiPP) natural products. Three NMR structures (glycocin F, ASM1 and sublancin 168), two with helix-loop-helix Cs alpha/alpha folds, are deposited in the PDB. Each structure contains a monosaccharide beta-S-linked to a cysteine side chain. Three more glycocins (thurandacin, and enterocins F4-9 and 96) have been biochemically characterised, and others predicted on the basis of bioinformatic analyses. Only glycocin F, ASM1 and enterocin F4-9 are unequivocally glycoactive. This review probes the structure-function relationships of four types of nested disulfide-bonded glycocins.

关键词： enterocin Enterobactin structure-function relationships sublancin 168 Bacterial Toxins Subset lantibiotic H19 gene Classes Fluorine (F)

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Understanding the structure-function Relationship of Lysozyme Resistance in Staphylococcus aureus by Peptidoglycan O-Acetylation Using Molecular Docking, Dynamics, and Lysis Assay

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JOURNAL OF CHEMICAL INFORMATION AND MODELING 2015年第4期55卷 760-770页

作者： Pushkaran, Anju C. Nataraj, Namrata Nair, Nisha Goetz, Friedrich Biswas, Raja Mohan, C. Gopi Amrita Vishwa Vidyapeetham Univ Amrita Ctr Nanosci & Mol Med Amrita Inst Med Sci Kochi 682041 Kerala India Amrita Vishwa Vidyapeetham Univ Res Ctr Kochi 682041 Kerala India Univ Tubingen Microbial Genet Interfac Inst Microbiol & Infect Med Tubingen IMI D-72074 Tubingen Germany

Lysozyme is an important component of the host innate defense system. It cleaves the beta-1,4 glycosidic bonds between N-acetylmuramic acid and N-acetylglucosamine of bacterial peptidoglycan and induce bacterial lysis. Staphylococcus aureus (S. aureus), an opportunistic commensal pathogen, is highly resistant to lysozyme, because of the O-acetylation of peptidoglycan by O-acetyl transferase (oatA). To understand the structure-function relationship of lysozyme resistance in S. aureus by peptidoglycan O-acetylation, we adapted an integrated approach to (i) understand the effect of lysozyme on the growth of S. aureus parental and the oatA mutant strain, (ii) study the lysozyme induced lysis of exponentially grown and stationary phase of both the S. aureus parental and oatA mutant strain, (iii) investigate the dynamic interaction mechanism between normal (de-O-acetylated) and O-acetylated peptidoglycan substrate in complex with lysozyme using molecular docking and molecular dynamics simulations, and (iv) quantify lysozyme resistance of S. aureus parental and the oatA mutant in different human biological fluids. The results indicated for the first time that the active site cleft of lysozyme binding with O-acetylated peptidoglycan in S. aureus was sterically hindered and the structural stability was higher for the lysozyme in complex with normal peptidoglycan. This could have conferred reduced survival of the S. aureus oatA mutant in different human biological fluids. Consistent with this computational analysis, the experimental data confirmed decrease in the growth, lysozyme induced lysis, and lysozyme resistance, due to peptidoglycan O-acetylation in S. aureus.

关键词： Sulfur Staphylococcus aureus Peptidoglycan structure-function relationships Tissue Lysis Muramidase molecular docking

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Studium receptorů pro opioidy

Studium receptorů pro opioidy

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作者： Cechová, Kristína Charles University of Prague

1 ABSTRACT In this Thesis, we studied properties of μ-, δ-, and κ-opioid receptors in lymphocytes isolated from rat spleen. This splenocytes were exposed to mitogen concanavalin A or opiate morphine and cultivated for 48 hours. Under physiological conditions, level of opioid receptors in immune cells is very low. Due to various factors such as presence of opioids, mitogens, long-term exposition to stress, expression of these receptors can be amplified. In this study we demonstrated, that concanavalin A causes up-regulation of μ-, δ- and κ-opioid receptors in lymphocytes isolated from rat spleen. In control cells no significant signal of μ- or δ-receptors was observed. In contrast, κ-opioid receptors were detected already in control cells. Concanavalin A stimulation caused a 2.4 - fold increase of these receptors. In lymphocytes treated with morphine only μ-opioid receptors were up-regulated, whereas in control cells, there was no signal for these receptor type. δ-opioid receptors were not detected in control or morphine treated cells. κ-opioid receptors were determined in control and also in morphine affected lymphocytes but the amount of these receptors wasnt changed by morphine. Detection of μ-, δ- and κ-opioid receptors using Western blot technique in lymphocytes isolated from rat spleen, that were...

关键词： opioid receptors structure-function relationships

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structure-function relationships to guide rational design and fabrication of particulate food delivery systems

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TRENDS IN FOOD SCIENCE & TECHNOLOGY 2009年第10期20卷 448-457页

作者： Lesmes, Uri McClements, David Julian Univ Massachusetts Dept Food Sci Food Biopolymers & Colloids Res Lab Amherst MA 01003 USA

The rational design and fabrication of food-grade delivery systems can draw extensively from the knowledge gained through the development of drug delivery systems. This review provides a concise overview of particulate delivery systems and outlines current research trends linking their structural properties to their functionality, e.g., matrix compatibility, stability, release characteristics and bioavailability. The need to establish quantitative structure-function relationships (QSFR) between particle properties and delivery system functionality is highlighted for the efficient development of food-grade delivery systems in the future.

关键词： PARTICULATE FOODS structure functionAL PROPERTIES PARTICLES REVIEWS fabrication structure-function relationships Research trends functional characteristics rational design DELIVERY SYSTEM FOOD DELIVERY SYSTEMS Drug Liberation

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Corrosion inhibition of mild steel in hydrochloric acid solution by quaternary ammonium salt derivatives of corn stalk polysaccharide (QAPS)

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DESALINATION 2015年 372卷 57-66页

作者： Zhang, Huixin Wang, Dongdong Wang, Feng Jin, Xiuhong Yang, Tingru Cai, Zhiyue Zhang, Jie Hebei Univ Technol Sch Chem & Chem Engn Tianjin 300130 Peoples R China Cent Res Inst China Chem Sci & Technol Beijing 100083 Peoples R China CNOOC Tianjin Res & Design Inst Chem Ind Tianjin 300131 Peoples R China

Novel phosphorus-free corn stalk polysaccharide (PS) derivatives were prepared using 2,3-epoxypropyltrimethylammonium chloride, N-methyl imidazole, pyridine and epichlorohydrin as starting materials. The corrosion inhibition performance with their adsorption mechanisms for mild steel was studied in 1.0 mol/L HCl solution by a series of techniques such as weight loss, potentiodynamic polarization curves, electrochemical impedance spectroscopy (EIS), electron scanning microscope (SEM) and XPS analysis. The values of apparent activation energy (E-a) for mild steel corrosion and Delta G(0), Delta H-0 and Delta S-0 were calculated and discussed. The results suggested that the inhibitors were mixed ones with predominant anodic inhibition and the corrosion behavior in the presence of QAPSs can been explained by the adsorption film mechanism. Moreover, the adsorption process obeys Langmuir adsorption isotherm model and the N, C atoms of the heterocycle and the O atom of the hydroxyl group combined with the Fe element from the XPS spectra. (C) 2015 Elsevier B.V. All rights reserved.

关键词： Acid corrosion Corn stalk polysaccharide derivatives SEM structure-function relationships EIS

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Pendant allyl crosslinking as a tunable shape memory actuator for vascular applications

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ACTA BIOMATERIALIA 2015年 24卷 53-63页

作者： Boire, Timothy C. Gupta, Mukesh K. Zachman, Angela L. Lee, Sue Hyun Balikov, Daniel A. Kim, Kwangho Bellan, Leon M. Sung, Hak-Joon Vanderbilt Univ Dept Biomed Engn Nashville TN 37235 USA Vanderbilt Univ Inst Chem Biol Nashville TN 37235 USA Vanderbilt Univ Dept Mech Engn Nashville TN 37235 USA

Thermo-responsive shape memory polymers (SMPs) can be programmed to fit into small-bore incisions and recover their functional shape upon deployment in the body. This property is of significant interest for developing the next generation of minimally-invasive medical devices. To be used in such applications, SMPs should exhibit adequate mechanical strengths that minimize adverse compliance mismatch-induced host responses (e.g. thrombosis, hyperplasia), be biodegradable, and demonstrate switch-like shape recovery near body temperature with favorable biocompatibility. Combinatorial approaches are essential in optimizing SMP material properties for a particular application. In this study, a new class of thermo-responsive SMPs with pendant, photocrosslinkable allyl groups, x%poly(epsilon-caprolac tone)-co-y%(alpha-allyl carboxylate e-caprolactone) (x%PCL-y%ACPCL), are created in a robust, facile manner with readily tunable material properties. Thermomechanical and shape memory properties can be drastically altered through subtle changes in ally! composition. Molecular weight and gel content can also be altered in this combinatorial format to fine-tune material properties. Materials exhibit highly elastic, switch-like shape recovery near 37 degrees C. Endothelial compatibility is comparable to tissue culture polystyrene (TCPS) and 100%PCL in vitro and vascular compatibility is demonstrated in vivo in a murine model of hindlimb ischemia, indicating promising suitability for vascular applications. Statement of Significance With the ongoing thrust to make surgeries minimally-invasive, it is prudent to develop new biomaterials that are highly compatible and effective in this workflow. Thermo-responsive shape memory polymers (SMPs) have great potential for minimally-invasive applications because SMP medical devices (e.g. stents, grafts) can fit into small-bore minimally-invasive surgical devices and recover their functional shape when deployed in the body. To realize their po

关键词： Allylic compounds Shape memory polymers Thermally responsive materials structure-function relationships Biocompatibility

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NMR Approaches to functional Dynamics of Genetically Separated iGluR Domains

NMR Approaches to Functional Dynamics of Genetically Separat...

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作者： Christopher P. Ptak Ahmed H. Ahmed Robert E. Oswald

Neurotransmitter receptor channels, such as ionotropic glutamate receptors, are proteins whose functional activity requires specific motions in response to the binding of small ligands. In order to understand how these proteins work, it is important not only to know the three-dimensional structure at atomic resolution but also to understand, at the atomic level, these characteristic motions. An important strength of the analysis of proteins with NMR spectroscopy is the detection of motions of individual atoms on a broad variety of timescales. The drawback is that relatively large concentrations of protein are required and, to a large extent, the size of the complex can be limiting. We describe here the production and isotopic labeling of the ligand-binding domain of an AMPA receptor (GluA2) to permit studies of protein dynamics by NMR. The strategies for resonance assignment and the experiments used to study dynamics are also described. less

关键词： NMR Isotope Labeling Nickel Affinity Chromatography 2D NMR Spectroscopy HNCO HNCA Pulsed NMR Specific Labeling Fluorine-19 Magnetic Resonance Spectroscopy 1D NMR Spectroscopy Drug Screening And Discovery Saccharomyces cerevisiae Protein dynamics AMPA receptors Ionotropic glutamate receptors GluA2 structure-function relationships

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Precisely Tailoring the Stoichiometric Stacking of Perylene-TCNQ Co-Crystals towards Different Nano and Microstructures with Varied Optoelectronic Performances

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SMALL 2015年第18期11卷 2150-2156页

作者： Zhu, Weigang Yi, Yuanping Zhen, Yonggang Hu, Wenping Chinese Acad Sci Inst Chem Lab Organ Solids Beijing 100190 Peoples R China Univ Chinese Acad Sci Beijing 100049 Peoples R China

Organic charge-transfer co-crystals with varied donor-acceptor stoichiometric ratios and molecular packing structures are controllably prepared with the morphology of nanowires or microblocks. They have distinct charge transport behavior and photoresponsivity. These interesting results pave the way for rational design and preparation of co-crystals with desired functions.

关键词： charge-transfer complexes organic co-crystals self-assembly structure-function relationships

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Insights into the preferential order of strand exchange in the Cre/loxP recombinase system: impact of the DNA spacer flanking sequence and flexibility

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JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN 2015年第3期29卷 271-282页

作者： Abi-Ghanem, Josephine Samsonov, Sergey A. Pisabarro, M. Teresa Biotec TU Dresden D-01037 Dresden Germany

The Cre/loxP system is widely used as a genetic tool to manipulate DNA. Cre recombinase catalyzes site-specific recombination between 34 bp loxP sites. Each loxP site is recognized by two Cre molecules assuming a cleaving (Cre(C)) and non-cleaving (Cre(NC)) activity. Despite the symmetry in the sequences of the arms of loxP, available biochemical data show strong evidence that the recombination reaction is asymmetric with a preferred strand exchange order. The asymmetry comes from the spacer separating the two sets of palindromic arms of the loxP sequence. However, it remains to be understood how this preferential order is established. We apply computational structure-based methods and perform a thorough detailed analysis of available structural and biochemical information on the Cre/loxP system in order to investigate such asymmetry in the recombination, and we propose a rationale to explain the determinants favoring the strand exchange order. We show that the structural properties of the DNA flanking sequence of the spacer guide the recombination, and we establish the role of residues R118, R121 and K122 from Cre(C), which contact the spacer region and by clamping the DNA inhibit the cleavage on the second arm of loxP. Our studies give an atomistic insight on the synapsis state of the recombination process in the Cre/loxP system and highlight the importance of the flexibility and other intrinsic properties of the flanking regions of the DNA spacer to establish a preferential strand exchange order.

关键词： structure-function relationships Cre recombinase DNA strand exchange DNA flexibility Molecular dynamics

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