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Oxidative aliphatic carbon-carbon bond cleavage reactions

COORDINATION CHEMISTRY REVIEWS 2013年第21-22期257卷 3005-3029页

作者： Allpress, Caleb J. Berreau, Lisa M. Utah State Univ Dept Chem & Biochem Logan UT 84322 USA

Over the past decade, several metalloenzymes have been characterized which catalyze dioxygenase-type aliphatic carbon-carbon bond cleavage reactions. The substrates for these enzymes vary from species that are stable with respect to O-2 under ambient conditions, to examples that in anionic form exhibit O-2 reactivity in the absence of enzyme. Described herein are advances from studies of the enzymes themselves and model systems. These combined investigations provide insight into novel mechanistic pathways leading to aliphatic carbon-carbon bond cleavage and/or the factors that influence regioselectivity in the oxidative carbon-carbon bond cleavage reactions. (C) 2013 Elsevier B.V. All rights reserved.

关键词： Dioxygen activation Bioinorganic chemistry Dioxygenase Enzyme catalysis Carbon monoxide structure-function relationships

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Characterization of a multifunctional α2,3-sialyltransferase from Pasteurella dagmatis

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GLYCOBIOLOGY 2013年第11期23卷 1293-1304页

作者： Schmoelzer, Katharina Ribitsch, Doris Czabany, Tibor Luley-Goedl, Christiane Kokot, Deja Lyskowski, Andrzej Zitzenbacher, Sabine Schwab, Helmut Nidetzky, Bernd Austrian Ctr Ind Biotechnol A-8010 Graz Austria Graz Univ Technol Inst Biotechnol & Biochem Engn A-8010 Graz Austria Graz Univ Technol Inst Mol Biotechnol A-8010 Graz Austria

A new multifunctional alpha 2,3-sialyltransferase has been discovered in Pasteurella dagmatis. The enzyme, in short PdST, was identified from the P. dagmatis genome by sequence similarity with sialyltransferases of glycosyltransferase family GT-80. In addition to its regioselective sialyltransferase activity (5.9 U/mg;pH 8.0), purified PdST is alternatively active at low pH as alpha 2,3-sialidase (0.5 U/mg;pH 4.5) and alpha 2,3-trans-sialidase (1.0 U/mg;pH 4.5). It also shows cytidine-5'-monophosphate N-acetyl-neuraminic (CMP-Neu5Ac) hydrolase activity (3.7 U/mg;pH 8.0) when no sialyl acceptor substrate is present in the reaction. After sialyltransferase PmST1 from P. multocida, PdST is the second member of family GT-80 to display this remarkable catalytic promiscuity. A unique feature of PdST, however, is a naturally occurring Ser-to-Thr substitution within a highly conserved Y(112)DDGS(116) sequence motif. In PmST1, the equivalent Ser(143) is involved in binding of the CMP-Neu5Ac donor substrate. Reversion of the natural mutation in a T116S-PdST variant resulted in a marked increase in alpha 2,3-trans-sialidase side activity (4.0 U/mg;pH 4.5), whereas the major sialyltransferase activity was lowered (3.8 U/mg;pH 8.0). The Michaelis-Menten constant for CMP-Neu5Ac was decreased 4-fold in T116S mutant when compared with wild-type PdST (K-M=1.1 mM), indicating that residue 116 of PdST contributes to a delicate balance between substrate binding and catalytic activity. D-Galactose and various beta-D-galactosides function as sialyl acceptors from CMP-Neu5Ac, whereas other hexoses (e. g. D-glucose) are inactive. structure comparison was used to rationalize the particular acceptor substrate specificity of PdST in relation to other GT-80 sialyltransferases that show strict alpha 2,3-regioselectivity, but are flexible in using alpha/beta-galactosides for sialylation.

关键词： bacterial sialyltransferase glycosyltransferase family GT-80 natural mutation N-terminal elongation structure-function relationships

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Microphytobenthos in Shallow Arctic Lakes: Fine-Scale Depth Distribution of Chlorophyll a, Radiocarbon Assimilation, Irradiance, and Dissolved O₂

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ARCTIC ANTARCTIC AND ALPINE RESEARCH 2013年第2期45卷 285-295页

作者： Whalen, Stephen C. Lofton, Dendy D. McGowan, Gabriel E. Strohm, Amy Univ N Carolina Dept Environm Sci & Engn Chapel Hill NC 27599 USA

We compared in three shallow Alaskan Arctic lakes physical properties of bulk sediment and the fine-scale (1 mm increments to 20 mm sediment depth) vertical distribution of dissolved 02, scalar irradiance, chlorophyll a, and radiocarbon assimilation by microphyto-benthos to better understand the structural and functional significance of this community. Sediments showed water contents of 86-98%, and dry bulk densities of 0.012-0.146 g cm(-3), depending on depth. Chlorophyll a displayed no clear vertical pattern, suggesting mixing of surface layers and showed lakewise averages of 5.1-23.7 mu g cm(-3). Sediments were oxic to 1.5-5.5 mm and showed attenuation coefficients of 1.17-2.07 mm(-1) for photon scalar irradiance. Photosynthetic activity was localized near the sediment surface, as 57-81% of (HCO3-)-C-14 added to intact cores was recovered in the 0-2 mm zone. Only 26-44% of the chlorophyll a in vertical profiles was sited in the euphotic zone, but microphytobenthos in underlying, aphotic sediments immediately photosynthesized at or near rates for the surface sediment when artificially irradiated. Area-based chlorophyll a in the euphotic plus photosynthetically capable aphotic microphytobenthos was 62-105 times higher than that of the phytoplankton, pointing to the potential importance of benthic autotrophs to Arctic lake food webs.

关键词： Physical properties Vertical distribution Chlorophylls Phytobenthos Irradiance Extinction coefficient Surface layers Food webs Vertical profiles Lakes Chlorophyll Cores Photons structure-function relationships Phytoplankton Water content Sediments Attenuation coefficients Arctic lakes Marine sediment cores Data assimilation Food Chains Chlorophyll A Density Physical Properties Vertical Distribution Mixing Arctic

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Dynamic and structural constraints in signal propagation by regulatory networks

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MOLECULAR BIOSYSTEMS 2013年第2期9卷 268-284页

作者： Estrada, Javier Guantes, Raul Univ Autonoma Madrid Dept Condensed Matter Phys E-28049 Madrid Spain Univ Autonoma Madrid Fac Ciencias Mat Sci Inst Nicolas Cabrera E-28049 Madrid Spain

Regulatory networks are able to process complex signals and respond appropriately to the cellular context. Thus, an increasing effort by systems biology researchers is being focused on understanding which interactions are responsible for a given functional response. When translated into specific mathematical models, however, it has been repeatedly shown that this mapping between topology and function is not one-to-one, even for the simplest networks. Moreover, dynamical behavior may play an important role which is necessary to integrate in the general picture. We propose a unified theoretical/statistical approach to characterize the structure-function relationship in molecular networks when temporal features of both input signal and output response are important. The theory allows fast computation of network responses in terms of interaction strengths irrespective of molecular details, while statistical analysis identifies constraints between structural and dynamical features and network function. Investigating different feedback and feedforward loop architectures, we find that processing of temporal signals is strongly correlated to certain combinations of structural and dynamical characteristics, rather than to individual interactions. Our analysis offers new insight into the structure-function relationship in network motifs, quantifying how much the tuning of specific interactions affects network outcome, identifying key structural parameters for a given response and relating dynamics to network topology and function. This kind of analyses can be especially useful for synthetic biology approaches, where promoter libraries with a range of inputs and outputs can be engineered, and one has to choose the correct component needed to produce the desired network function.

关键词： structure-function relationships Regulatory Network topology signals Network input signal complex signal

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The chemistry of low dosage clathrate hydrate inhibitors

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CHEMICAL SOCIETY REVIEWS 2013年第5期42卷 1996-2015页

作者： Perrin, Andrea Musa, Osama M. Steed, Jonathan W. Univ Durham Dept Chem Durham DH1 3LE England Ashland Special Ingredients Wayne NJ 07470 USA

This review aims to introduce the chemistry of low dosage inhibitors of clathrate hydrate formation within the context of their role in the oil and gas industry. The review covers both kinetic hydrate inhibitors and anti-agglomerants from the point of view of structure-function relationships, focussing on recent refinements in mechanistic understanding and chemical design, and the consequently evolving and increasingly fine-tuned properties of these fascinating compounds.

关键词： Oil and Gas Industry structure-function relationships gas industry Chemistry clathrate HYDRATE INHIBITOR point of view

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Biomineralization proteins： from vertebrates to bacteria

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Frontiers in Biology 2013年第2期8卷 234-246页

作者： Lijun WANG Marit NILSEN-HAMILTON Ames Laboratory U. S. Department of Energy Department of Biochemistry Biophysics and Molecular Biology Iowa State University AmesIA 50011 USA

Biomineralization processes are frequently found in nature. Living organisms use various strategies to create highly ordered and hierarchical mineral structures under physiologic conditions in which the temperatures and pressures are much lower than those required to form the same mineralized structures by chemical synthesis. Although the mechanism of biomineralization remains elusive, proteins have been found responsible for the formation of such mineral structures in many cases. These proteins are active components in the process of biomineralization. The mechanisms by which their function can vary from providing active organic matrices that control the formation of specific mineral structures to being catalysts that facilitate the crystallization of certain metal ions. This review summarizes the current understanding of the functions of several representative biomineralization proteins from vertebrates to bacteria in the hopes of providing useful insight and guidance for further elucidation of mechanisms of biomineralization processes in living organisms.

关键词： biomineralization proteins structure-function relationships self-assembly nanoparticles

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Is the Link between Anatomical structure and function Equally Strong at All Cognitive Levels of Processing?

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CEREBRAL CORTEX 2012年第7期22卷 1593-1603页

作者： Tahmasebi, Amir M. Davis, Matthew H. Wild, Conor J. Rodd, Jennifer M. Hakyemez, Helene Abolmaesumi, P. Johnsrude, Ingrid S. Baycrest Ctr Geriatr Care Rotman Res Inst Toronto ON M6A 2E1 Canada MRC Cognit & Brain Sci Unit Cambridge CB2 2EF England Queens Univ Ctr Neurosci Studies Kingston ON K7L 3N6 Canada UCL Dept Cognit Perceptual & Brain Sci London WC1H 0AP England Queens Univ Dept Psychol Kingston ON K7L 3N6 Canada Univ British Columbia Dept Elect & Comp Engn Vancouver BC V6T 1Z4 Canada Linkoping Univ Linnaeus Ctr Hearing & Deafness SE-58183 Linkoping Sweden

Whereas low-level sensory processes can be linked to macroanatomy with great confidence, the degree to which high-level cognitive processes map onto anatomy is less clear. If function respects anatomy, more accurate intersubject anatomical registration should result in better functional alignment. Here, we use auditory functional magnetic resonance imaging and compare the effectiveness of affine and nonlinear registration methods for aligning anatomy and functional activation across subjects. Anatomical alignment was measured using normalized cross-correlation within functionally defined regions of interest. functional overlap was assessed using t-statistics from the group analyses and the degree to which group statistics predict high and consistent signal change in individual data sets. In regions related to early stages of auditory processing, nonlinear registration resulted in more accurate anatomical registration and stronger functional overlap among subjects compared with affine. In frontal and temporal areas reflecting high-level processing of linguistic meaning, nonlinear registration also improved the accuracy of anatomical registration. However, functional overlap across subjects was not enhanced in these regions. Therefore, functional organization, relative to anatomy, is more variable in the frontal and temporal areas supporting meaning-based processes than in areas devoted to sensory/perceptual auditory processing. This demonstrates for the first time that functional variability increases systematically between regions supporting lower and higher cognitive processes.

关键词： anatomy fMRI functional variability hearing image normalization language lexical ambiguity semantic processing speech perception structure-function relationships

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Comparative analysis of inner cavities and ligand migration in non-symbiotic AHb1 and AHb2

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BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013年第9期1834卷 1957-1967页

作者： Spyrakis, Francesca Lucas, Fatima Bidon-Chanal, Axel Viappiani, Cristiano Guallar, Victor Luque, F. Javier Univ Parma Dipartimento Sci Alimenti I-43100 Parma Italy Barcelona Supercomp Ctr Joint BSC IRB Res Program Computat Biol Barcelona Spain Univ Barcelona Dept Fis Quim Fac Farm Santa Coloma De Gramenet Spain Univ Barcelona Inst Biomed IBUB Santa Coloma De Gramenet Spain Univ Parma Dipartimento Fis & Sci Terra I-43100 Parma Italy ICREA Barcelona Spain

This study reports a comparative analysis of the topological properties of inner cavities and the intrinsic dynamics of non-symbiotic hemoglobins AHb1 and AHb2 from Arabidopsis thaliana. The two proteins belong to the 3/3 globin fold and have a sequence identity of about 60%. However, it is widely assumed that they have distinct physiological roles. In order to investigate the structure-function relationships in these proteins, we have examined the bis-histidyl and ligand-bound hexacoordinated states by atomistic simulations using in silico structural models. The results allow us to identify two main pathways to the distal cavity in the bis-histidyl hexacoordinated proteins. Nevertheless, a larger accessibility to small gaseous molecules is found in AHb2. This effect can be attributed to three factors: the mutation Leu35(AHb1) -> Phe32(AHb2), the enhanced flexibility of helix B, and the more favorable energetic profile for ligand migration to the distal cavity. The net effect of these factors would be to facilitate the access of ligands, thus compensating the preference for the fully hexacoordination of AHb2, in contrast to the equilibrium between hexa- and pentacoordinated species in AHb1. On the other hand, binding of the exogenous ligand introduces distinct structural changes in the two proteins. A well-defined tunnel is formed in AHb1, which might be relevant to accomplish the proposed NO detoxification reaction. In contrast, no similar tunnel is found in AHb2, which can be ascribed to the reduced flexibility of helix E imposed by the larger number of salt bridges compared to AHb1. This feature would thus support the storage and transport functions proposed for AHb2. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins. (c) 2013 Elsevier B.V. All rights reserved.

关键词： Non-symbiotic hemoglobins Ligand migration Protein flexibility structure-function relationships Molecular simulations

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Intersubunit Bridge Formation Governs Agonist Efficacy at Nicotinic Acetylcholine α4β2 Receptors UNIQUE ROLE OF HALOGEN BONDING REVEALED

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JOURNAL OF BIOLOGICAL CHEMISTRY 2012年第6期287卷 4248-4259页

作者： Rohde, Line Aagot Hede Ahring, Philip Kiaer Jensen, Marianne Lerbech Nielsen, Elsebet Ostergaard Peters, Dan Helgstrand, Charlotte Krintel, Christian Harpsoe, Kasper Gajhede, Michael Kastrup, Jette Sandholm Balle, Thomas Univ Copenhagen Dept Med Chem Fac Pharmaceut Sci DK-2100 Copenhagen Denmark NeuroSearch AS DK-2750 Ballerup Denmark

The alpha 4 beta 2 subtype of the nicotinic acetylcholine receptor has been pursued as a drug target for treatment of psychiatric and neurodegenerative disorders and smoking cessation aids for decades. Still, a thorough understanding of structure-function relationships of alpha 4 beta 2 agonists is lacking. Using binding experiments, electrophysiology and x-ray crystallography we have investigated a consecutive series of five prototypical pyridine-containing agonists derived from 1-(pyridin-3-yl)-1,4-diazepane. A correlation between binding affinities at alpha 4 beta 2 and the acetylcholine-binding protein from Lymnaea stagnalis (Ls-AChBP) confirms Ls-AChBP as structural surrogate for alpha 4 beta 2 receptors. Crystal structures of five agonists with efficacies at alpha 4 beta 2 from 21-76% were determined in complex with Ls-AChBP. No variation in closure of loop C is observed despite large efficacy variations. Instead, the efficacy of a compound appears tightly coupled to its ability to form a strong intersubunit bridge linking the primary and complementary binding interfaces. For the tested agonists, a specific halogen bond was observed to play a large role in establishing such strong intersubunit anchoring.

关键词： Agonist Nicotinic Acetylcholine Drug Liberation structure-function relationships Smoking Cessation Neurodegenerative Diseases halogens Nicotinic Receptors

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Streamlined access to conjugation-ready glycans by automated synthesis

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CHEMICAL SCIENCE 2012年第5期3卷 1617-1622页

作者： Kroeck, Lenz Esposito, Davide Castagner, Bastien Wang, Cheng-Chung Bindschaedler, Pascal Seeberger, Peter H. Max Planck Inst Colloids & Interfaces Dept Biomol Syst D-14476 Potsdam Germany Free Univ Berlin Inst Chem & Biochem D-14195 Berlin Germany

Understanding the structure-function relationship of carbohydrates in biological systems is a major challenge. Such investigations require fast and reliable access to structurally-defined oligosaccharides. To date, oligosaccharide synthesis has been considered technically difficult and only parts of the synthetic process have been automated using solution and solid-phase techniques. Here, we describe a versatile platform integrating a new synthesis strategy and a fully-automated oligosaccharide synthesizer. Structurally diverse conjugation-ready oligosaccharides can be generated for the creation of glycoconjugates and microarrays. Biologically-significant oligosaccharides of increasing length, structural complexity, and chemical diversity were produced, including glycans found on the surfaces of pathogenic bacteria, and those with integral roles in inflammatory and immune responses.

关键词： Oligosaccharides synthesis Surfaces structure-function relationships Polysaccharides Automation biological organs SYNTHETIC PROCESS Glycoconjugates Carbohydrates Pathogenic bacteria Access

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