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Protonation-Dependent Base Flipping at Neutral pH in the Catalytic Triad of a Self-Splicing Bacterial GroupII Intron

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ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 2015年第33期54卷 9687-9690页

作者： Pechlaner, Maria Donghi, Daniela Zelenay, Veronika Sigel, Roland K. O. Univ Zurich Dept Chem CH-8057 Zurich Switzerland

NMR spectroscopy has revealed pH-dependent structural changes in the highly conserved catalytic domain5 of a bacterial groupII intron. Two adenines with pK(a)values close to neutral pH were identified in the catalytic triad and the bulge. Protonation of the adenine opposite to the catalytic triad is stabilized within a G(syn)-AH(+)(anti) base pair. The pH-dependent anti-to-syn flipping of this G in the catalytic triad modulates the known interaction with the linker region between domains2 and 3 (J23) and simultaneously the binding of the catalytic Mg2+ ion to its backbone. Hence, this here identified shifted pK(a)value controls the conformational change between the two steps of splicing.

关键词： groupII introns NMR spectroscopy ribozymes RNA structure-function relationships

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Effect of Anion structures on Cholinium Ionic Liquids Pretreatment of Rice Straw and the Subsequent Enzymatic Hydrolysis

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BIOTECHNOLOGY AND BIOENGINEERING 2015年第1期112卷 65-73页

作者： Hou, Xue-Dan Xu, Jie Li, Ning Zong, Min-Hua S China Univ Technol Coll Light Ind & Food Sci State Key Lab Pulp & Paper Engn Guangzhou 510640 Guangdong Peoples R China S China Univ Technol Coll Biosci & Bioengn Guangzhou 510640 Guangdong Peoples R China

In this work, 28 cholinium ionic liquids (ILs), most of which are good solvents for dissolving lignin, were used for rice straw pretreatment to improve subsequent enzymatic hydrolysis. The anion exerted a significant effect on the pretreatment effectiveness of the IL as well as the subsequent enzymatic hydrolysis efficiency of rice straw residues. The presence of the basic group(s) in the anion significantly enhanced the IL pretreatment effectiveness, while the carboxyl, hydroxyl and aromatic groups had a negative impact on IL delignification. Except for amino acid-based ILs, the delignification abilities of the ILs are linearly and positively correlated with the pK(a) values of the conjugate acids of the anions. Of the ILs tested, amino acid-based ILs, especially basic amino acid-based ILs, are the most effective pretreatment solvents. Satisfactory reducing sugar yields (81% for glucose and 26% for xylose) were obtained in the enzymatic hydrolysis of rice straw pretreated by cholinium argininate ([Ch][Arg]) under a pretty mild pretreatment severity (60 degrees C, 6 h). The results presented in this work may be useful for rational design of novel and green ILs for delignification of lignocellulose. (C) 2014 Wiley Periodicals, Inc.

关键词： delignification enzymatic hydrolysis ionic liquids lignocellulosic biomass pretreatment structure-function relationships

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Probing the chemical mechanism and critical regulatory amino acid residues of Drosophila melanogaster arylalkylamine N-acyltransferase like 2

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INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2015年第0期66卷 1-12页

作者： Dempsey, Daniel R. Carpenter, Anne-Marie Ospina, Santiago Rodriguez Merkler, David J. Univ S Florida Dept Chem Tampa FL 33620 USA

Arylalkylamine N-acyltransferase like 2 (AANATL2) catalyzes the formation of N-acylarylalkylamides from the corresponding acyl-CoA and arylalkylamine. The N-acylation of biogenic amines in Drosophila melanogaster is a critical step for the inactivation of neurotransmitters, cuticle sclerotization, and melatonin biosynthesis. In addition, D. melanogaster has been used as a model system to evaluate the biosynthesis of fatty acid amides: a family of potent cell signaling lipids. We have previously showed that AANATL2 catalyzes the formation of N-acylarylakylamides, including long-chain N-acylserotonins and N-acyldopamines. Herein, we define the kinetic mechanism for AANATL2 as an ordered sequential mechanism with acetyl-CoA binding first followed by tyramine to generate the ternary complex prior to catalysis. Bell shaped k(cat,app) (acetyl-CoA) and (k(cat)/K-m)(app) - (acetyl-CoA) pH-rate profiles identified two apparent PKa,app values of -7.4 and -8.9 that are critical to catalysis, suggesting the AANATL2-catalyzed formation of N-acetyltyramine occurs through an acid/base chemical mechanism. Site-directed mutagenesis of a conserved glutamate that corresponds to the catalytic base for other D. melanogaster AANATL enzymes did not produce a substantial depression in the k(cat,app) value nor did it abolish the pK(a,app) value attributed to the general base in catalysis (pK(a) -7.4). These data suggest that AANATL2 catalyzes the formation of N-acylarylalkylamides using either different catalytic residues or a different chemical mechanism relative to other D. melanogaster AANATL enzymes. In addition, we constructed other site-directed mutants of AANATL2 to help define the role of targeted amino acids in substrate binding and/or enzyme catalysis. (C) 2015 Elsevier Ltd. All rights reserved.

关键词： AANATL2 Chemical mechanism structure-function relationships N-acyldopamines N-acylserotonins

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Crucial role of the orexin-B C-terminus in the induction of OX₁ receptor-mediated apoptosis: analysis by alanine scanning, molecular modelling and site-directed mutagenesis

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BRITISH JOURNAL OF PHARMACOLOGY 2015年第21期172卷 5211-5223页

作者： Nicole, Pascal Couvineau, Pierre Jamin, Nadege Voisin, Thierry Couvineau, Alain Paris Diderot Univ CRI INSERM U1149DHU UNITYFac Med Site Bichat F-75018 Paris France CEA Lab Prot & Syst Membranaires iBiTecS I2BC F-91191 Gif Sur Yvette France

Background and PurposeOrexins (A and B) are hypothalamic peptides that interact with OX1 and OX2 receptors and are involved in the sleep/wake cycle. We previously demonstrated that OX1 receptors are highly expressed in colon cancer tumours and colonic cancer cell lines where orexins induce apoptosis and inhibit tumour growth in preclinical animal models. The present study explored the structure-function relationships of orexin-B and OX1 receptors. Experimental ApproachThe contribution of all orexin-B residues in orexin-B-induced apoptosis was investigated by alanine scanning. To determine which OX1 receptor domains are involved in orexin-B binding and apoptosis, a 3D model of OX1 receptor docked to the orexin-B C-terminus (AA-20-28) was developed. Substitution of residues present in OX1 receptor transmembrane (TM) domains by site-directed mutagenesis was performed. Key ResultsAlanine substitution of orexin-B residues, L-11, L-15, A(22), G(24), I-25, L-26 and M-28, altered orexin-B's binding affinity. Substitution of these residues and of the Q(16), A(17), S-18, N-20 and T-27 residues inhibited apoptosis in CHO-S-OX1 receptor cells. The K-120, P-123, Y-124, N-318, K-321, F-340, T-341, H-344 and W-345 residues localized in TM2, TM3, TM6 and TM7 of OX1 receptors were shown to play a role in orexin-B recognition and orexin-B/OX1 receptor-induced apoptosis. Conclusions and ImplicationsThe C-terminus of orexin-B (i) plays an important role in its pro-apoptotic effect;and (ii) interacts with some residues localized in the OX1 receptor TM. This study defines the structure-function relationship for orexin-B recognition by human OX1 receptors and orexin-B/OX1 receptor-induced apoptosis, an important step for the future development of new agonist molecules.

关键词： Alanine Site-Directed Mutagenesis Orexin A Receptor structure-function relationships molecular model Orexin-B Cancer of Colon Orexins C-Terminus

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Structural origin of anisotropic transport in electrically conducting dichloroacetic acid-treated polymers

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ORGANIC ELECTRONICS 2014年第2期15卷 631-638页

作者： Mativetsky, Jeffrey M. Tarver, Jacob Yang, Xiaofang Koel, Bruce E. Loo, Yueh-Lin Princeton Univ Dept Chem & Biol Engn Princeton NJ 08544 USA

The post-deposition treatment of water-processable, polymer acid-templated conducting polymers with dichloroacetic acid has recently been shown to enhance in-plane conductivity by orders of magnitude. Here, we evaluate both the in-plane and out-of-plane conductivities of dichloroacetic acid-treated conducting polymer films, and track the accompanying evolution of film structure and composition. Films of poly(ethylene dioxythiophene)-poly(styrene sulfonic acid), PEDOT-PSS, exhibit improvements in both in-plane and out-of-plane conductivities following dichloroacetic acid treatment, associated with the removal of excess PSS from the surface. Conversely, polyaniline-poly(2-acrylamido- 2-methyl-1-propanesulfonic acid), PANI-PAAMPSA, films are characterized by high anisotropies in conductivity, with the in-plane conductivity being orders of magnitude higher following DCA treatment and the out-of-plane conductivity substantially lower after the same treatment. Our experiments indicate that this unusual electrical anisotropy results from a vertically inhomogeneous composition profile. (C) 2014 Published by Elsevier B.V.

关键词： Conducting polymer Electrical conductivity Anisotropy structure-function relationships Poly(ethylene dioxythiophene) Polyaniline

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On hydrodynamic methods for the analysis of the sizes and shapes of polysaccharides in dilute solution: A short review

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FOOD HYDROCOLLOIDS 2014年第Part3期42卷 318-334页

作者： Morris, Gordon A. Adams, Gary G. Harding, Stephen E. Univ Huddersfield Sch Appl Sci Huddersfield HD1 3DH W Yorkshire England Univ Nottingham Natl Ctr Macromol Hydrodynam Sch Biosci Loughborough LE12 5RD Leics England

Background: Polysaccharides and their derivatives are increasingly being used by the food, cosmetic and pharmaceutical industries: physical properties like size and conformation are important contributors to their performance. Discussion: Here the use of hydrodynamic tools such as sedimentation velocity, sedimentation equilibrium, size exclusion chromatography - multi-angle light scattering (SEC-MALS), and viscometry are considered highlighting some recent developments in methodology and the application of these to help better understand polysaccharide structure-function relationships. Conclusions: The size and shape of polysaccharides in solution can be estimated in a variety of ways. Molar masses and heterogeneities can be estimated to a good precision by sedimentation velocity, sedimentation equilibrium and SEC-MALS. An approximate idea of conformation and flexibility can be obtained from power-law coefficients and the Wales van Holde parameter. More sophisticated estimates can be obtained by combining methods together to yield the persistence length. (C) 2014 Elsevier Ltd. All rights reserved.

关键词： Polysaccharides Size Conformation structure-function relationships

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Synaptic bouton properties are tuned to best fit the prevailing firing pattern

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FRONTIERS IN COMPUTATIONAL NEUROSCIENCE 2014年第September期8卷 101页

作者： Knodel, Markus M. Geiger, Romina Ge, Lihao Bucher, Daniel Grillo, Alfio Wittum, Gabriel Schuster, Christoph M. Queisser, Gillian Heidelberg Univ Bernstein Grp Detailed Modeling Signal Proc Neuro Heidelberg Germany Goethe Univ Frankfurt Heidelberg Germany Goethe Univ Frankfurt Goethe Ctr Sci Comp Dept Simulat & Modeling D-60325 Frankfurt Germany Bernstein Ctr Computat Neurosci Heidelberg Mannhe Heidelberg Germany Heidelberg Univ Dept Neurobiol Interdisciplinary Ctr Neurosci Heidelberg Germany European Mol Biol Lab Dev Unit D-69012 Heidelberg Germany Politecn Torino Dept Math Sci Turin Italy Goethe Univ Frankfurt Goethe Ctr Sci Comp Dept Computat Neurosci D-60325 Frankfurt Germany

The morphology of presynaptic specializations can vary greatly ranging from classical single-release-site boutons in the central nervous system to boutons of various sizes harboring multiple vesicle release sites. Multi-release-site boutons can be found in several neural contexts, for example at the neuromuscular junction (NMJ) of body wall muscles of Drosophila larvae. These NMJs are built by two motor neurons forming two types of glutamatergic multi-release-site boutons with two typical diameters. However, it is unknown why these distinct nerve terminal configurations are used on the same postsynaptic muscle fiber. To systematically dissect the biophysical properties of these boutons we developed a full three-dimensional model of such boutons, their release sites and transmitter-harboring vesicles and analyzed the local vesicle dynamics of various configurations during stimulation. Here we show that the rate of transmission of a bouton is primarily limited by diffusion-based vesicle movements and that the probability of vesicle release and the size of a bouton affect bouton-performance in distinct temporal domains allowing for an optimal transmission of the neural signals at different time scales. A comparison of our in silico simulations with in vivo recordings of the natural motor pattern of both neurons revealed that the bouton properties resemble a well-tuned cooperation of the parameters release probability and bouton size, enabling a reliable transmission of the prevailing firing-pattern at diffusion-limited boutons. Our findings indicate that the prevailing firing-pattern of a neuron may determine the physiological and morphological parameters required for its synaptic terminals.

关键词： neuromuscular junction boutons modeling and simulation structure-function relationships morphology firing pattern adaption

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On-Top π-Stacking of Quasiplanar Molecules in Hole-Transporting Materials: Inducing Anisotropic Carrier Mobility in Amorphous Films

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ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 2014年第23期53卷 5800-5804页

作者： Wakamiya, Atsushi Nishimura, Hidetaka Fukushima, Tatsuya Suzuki, Furitsu Saeki, Akinori Seki, Shu Osaka, Itaru Sasamori, Takahiro Murata, Michihisa Murata, Yasujiro Kaji, Hironori Kyoto Univ Inst Chem Res Uji Kyoto 6110011 Japan Osaka Univ Grad Sch Engn Dept Appl Chem Suita Osaka 5650871 Japan RIKEN CEMS Emergent Mol Funct Res Grp Wako Saitama 3510198 Japan

Dimers of partially oxygen-bridged triarylamines were designed and synthesized as hole-transporting materials. X-ray structural analyses revealed that these compounds form on-top pi-stacking aggregates in the crystalline state. TRMC measurements showed that high levels of anisotropic charge transport were induced in the direction of the pi-stacking. Surprisingly, even in vacuum-deposited amorphous films, these compounds retained some of the face-on pi-stacking, thus facilitating an out-of-plane carrier mobility.

关键词： amorphous materials heterocycles semiconductors structure-function relationships structure elucidation

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Development of Multinuclear Polymeric Nanoparticles as Robust Protein Nanocarriers

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ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 2014年第34期53卷 8975-8979页

作者： Wu, Jun Kamaly, Nazila Shi, Jinjun Zhao, Lili Xiao, Zeyu Hollett, Geoffrey John, Rohit Ray, Shaunak Xu, Xiaoyang Zhang, Xueqing Kantoff, Philip W. Farokhzad, Omid C. Harvard Univ Brigham & Womens Hosp Sch Med Lab Nanomed & BiomatDept Anesthesiol Boston MA 02115 USA MIT MIT Harvard Ctr Canc Nanotechnol Excellence Cambridge MA 02139 USA King Abdulaziz Univ Jeddah 22254 Saudi Arabia Nanjing Univ Sch Life Sci Nanjing 210093 Jiangsu Peoples R China Harvard Univ Sch Med Danan Farber Canc Inst Lank Ctr Genitourinary Oncol Boston MA 02115 USA

One limitation of current biodegradable polymeric nanoparticles is their inability to effectively encapsulate and sustainably release proteins while maintaining protein bioactivity. Here we report the engineering of PLGA-polycation nanoparticles with a core shell structure that act as a robust vector for the encapsulation and delivery of proteins and peptides. The optimized nanoparticles can load high amounts of proteins (>20% of nanoparticles by weight) in aqueous solution without organic solvents through electrostatic interactions by simple mixing, thereby forming nanospheres in seconds with diameters <200 nm. The relationship between nanosphere size, surface charge, PLGA-polycation composition, and protein loading is also investigated. The stable nanosphere complexes contain multiple PLGA-polycation nanoparticles, surrounded by large amounts of protein. This study highlights a novel strategy for the delivery of proteins and other relevant molecules.

关键词： nanoparticles polycations polymers protein delivery structure-function relationships

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Auditory-prefrontal axonal connectivity in the macaque cortex: Quantitative assessment of processing streams

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BRAIN AND LANGUAGE 2014年 135卷 73-84页

作者： Bezgin, Gleb Rybacki, Konrad van Opstal, A. John Bakker, Rembrandt Shen, Kelly Vakorin, Vasily A. McIntosh, Anthony R. Koetter, Rolf Univ Toronto Baycrest Ctr Rotman Res Inst Toronto ON M6A 2E1 Canada Radboud Univ Nijmegen Donders Inst Brain Cognit & Behav Dept Neuroinformat NL-6525 AJ Nijmegen Netherlands Univ Dusseldorf C&O Vogt Brain Res Inst D-40225 Dusseldorf Germany Univ Hosp Witten Herdecke HELIOS Med Ctr Wuppertal Dept Diagnost & Intervent Neuroradiol Wuppertal Germany Radboud Univ Nijmegen Donders Inst Brain Cognit & Behav Dept Biophys NL-6525 AJ Nijmegen Netherlands Res Ctr Julich Inst Neurosci & Med INM 6 Julich Germany Univ Munich Dept Biol 2 D-81377 Munich Germany Univ Dusseldorf Inst Comp Sci D-40225 Dusseldorf Germany Univ Toronto Dept Psychol Toronto ON M5S 3G3 Canada Univ Toronto Hosp Sick Children Toronto ON M5G 1X8 Canada

Primate sensory systems subserve complex neurocomputational functions. Consequently, these systems are organised anatomically in a distributed fashion, commonly linking areas to form specialised processing streams. Each stream is related to a specific function, as evidenced from studies of the visual cortex, which features rather prominent segregation into spatial and non-spatial domains. It has been hypothesised that other sensory systems, including auditory, are organised in a similar way on the cortical level. Recent studies offer rich qualitative evidence for the dual stream hypothesis. Here we provide a new paradigm to quantitatively uncover these patterns in the auditory system, based on an analysis of multiple anatomical studies using multivariate techniques. As a test case, we also apply our assessment techniques to more ubiquitously-explored visual system. Importantly, the introduced framework opens the possibility for these techniques to be applied to other neural systems featuring a dichotomised organisation, such as language or music perception. (C) 2014 Elsevier Inc. All rights reserved.

关键词： Auditory cortex Primate brain Sensory system Brain connectivity Parallel cortical pathways structure-function relationships Processing streams Prefrontal cortex Graph drawing Principal component analysis

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