This document summarizes the molecular mechanism of enzymatic allene oxide cyclization in plants. It discusses allene oxide cyclase (AOC), an enzyme that catalyzes the cyclization of 12,13-epoxy-9(Z),11,15(Z)-octadecatrienoic acid (12,13-EOT) to produce the oxylipin 12-oxo-phytodienoic acid (OPDA) in the jasmonic acid biosynthesis pathway. The review focuses on the crystal structure of AOC2 from Arabidopsis thaliana and putative binding sites for its unstable substrate 12,13-EOT. It also discusses possible intermolecular rearrangements during the cyclization reaction
Spps and side reactions in peptide synthesiskavyakaparthi1
The document discusses side reactions that can occur during solid phase peptide synthesis (SPPS). It describes several types of side reactions including proton abstraction, racemization through azlactone formation or direct abstraction, cyclization through diketopiperazine formation, and O-acylation. Racemization is a particular concern in SPPS since it changes the stereochemistry of amino acids. The document outlines factors that influence the likelihood of different side reactions such as the amino acid, solvent, and presence of tertiary amines. Understanding side reactions is important for planning and carrying out efficient SPPS.
1) Terpenes are derived from head-to-tail polymerization of isoprene units (C5). Monoterpenes contain 2 units, sesquiterpenes contain 3 units, and so on.
2) Mevalonic acid is converted to isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), the basic C5 units. Repeated condensation of these units leads to prenyl diphosphates of different sizes.
3) These prenyl diphosphates are converted by terpene synthases into the skeletons of various terpenes, which may then undergo further modifications. This
THE SOLID PHASE PEPTIDE SYNTHESIS IS SLIGHTLY DIFFRENT FROM PEPTIDE SYNTHESIS WHICH IS DISCUSSED HERE, ITS SYNTHESIS WITH STRUCTURE ANS BASICS ARE DISCUSSED WHICH WILL BE VERY USEFUL FOR READERS.
Biotransformation refers to the chemical alteration of substances within living organisms, typically involving enzymatic reactions. These reactions make compounds more water-soluble so they can be more easily excreted from the body. Biotransformation occurs in three phases - Phase I involves oxidation, reduction, and hydrolysis reactions; Phase II involves conjugating reactions like glucuronidation and sulfation; Phase III involves transport of conjugated compounds out of cells and organs. The liver is a major site of biotransformation, with cytochrome P450 enzymes and conjugating enzymes playing important roles in Phase I and Phase II reactions. Biotransformation is vital for the metabolism of drugs and other xenobiotics in the body.
This paper presents an efficient strategy to construct the core 7,7-fused ring system of colchicine using a sequential ring-closing metathesis approach, with the key steps being formylation of an intermediate followed by RCM reactions to form the bicyclic ring system in high yield; further transformations were carried out on this intermediate to synthesize additional ring structures found in colchicine via oxidative rearrangements. This route constitutes a formal synthesis of the natural product colchicine and investigation into fully completing the synthesis is ongoing.
The document discusses solid phase peptide synthesis (SPPS) methods using different protecting groups. It describes the t-Boc and Fmoc protecting group strategies, comparing their advantages and disadvantages. The t-Boc strategy uses acid-labile protecting groups removed by TFA, while the Fmoc strategy uses a base-labile Fmoc group and acid-labile side chain protecting groups, allowing milder acidic conditions. The document outlines the different protocols used in SPPS, including resin attachment, amino acid coupling and protecting group removal steps. It also discusses side reactions that can occur and strategies to minimize them, such as using orthogonal protecting groups or modified amino acid derivatives.
This document discusses peptide synthesis methods, including solution phase peptide synthesis and solid phase peptide synthesis (SPPS). SPPS involves attaching the starting peptide to an inert resin bead and performing sequential amino acid couplings and deprotections while the growing peptide remains attached to the resin. This allows for easy purification after each step. Once the full peptide is synthesized, it is cleaved off the resin bead. SPPS allows for faster synthesis of longer peptides up to 70-100 amino acids in length compared to solution phase synthesis. Applications of synthetic peptides include vaccines, hormones, antibiotics, toxins, and enzyme inhibitors.
Spps and side reactions in peptide synthesiskavyakaparthi1
The document discusses side reactions that can occur during solid phase peptide synthesis (SPPS). It describes several types of side reactions including proton abstraction, racemization through azlactone formation or direct abstraction, cyclization through diketopiperazine formation, and O-acylation. Racemization is a particular concern in SPPS since it changes the stereochemistry of amino acids. The document outlines factors that influence the likelihood of different side reactions such as the amino acid, solvent, and presence of tertiary amines. Understanding side reactions is important for planning and carrying out efficient SPPS.
1) Terpenes are derived from head-to-tail polymerization of isoprene units (C5). Monoterpenes contain 2 units, sesquiterpenes contain 3 units, and so on.
2) Mevalonic acid is converted to isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), the basic C5 units. Repeated condensation of these units leads to prenyl diphosphates of different sizes.
3) These prenyl diphosphates are converted by terpene synthases into the skeletons of various terpenes, which may then undergo further modifications. This
THE SOLID PHASE PEPTIDE SYNTHESIS IS SLIGHTLY DIFFRENT FROM PEPTIDE SYNTHESIS WHICH IS DISCUSSED HERE, ITS SYNTHESIS WITH STRUCTURE ANS BASICS ARE DISCUSSED WHICH WILL BE VERY USEFUL FOR READERS.
Biotransformation refers to the chemical alteration of substances within living organisms, typically involving enzymatic reactions. These reactions make compounds more water-soluble so they can be more easily excreted from the body. Biotransformation occurs in three phases - Phase I involves oxidation, reduction, and hydrolysis reactions; Phase II involves conjugating reactions like glucuronidation and sulfation; Phase III involves transport of conjugated compounds out of cells and organs. The liver is a major site of biotransformation, with cytochrome P450 enzymes and conjugating enzymes playing important roles in Phase I and Phase II reactions. Biotransformation is vital for the metabolism of drugs and other xenobiotics in the body.
This paper presents an efficient strategy to construct the core 7,7-fused ring system of colchicine using a sequential ring-closing metathesis approach, with the key steps being formylation of an intermediate followed by RCM reactions to form the bicyclic ring system in high yield; further transformations were carried out on this intermediate to synthesize additional ring structures found in colchicine via oxidative rearrangements. This route constitutes a formal synthesis of the natural product colchicine and investigation into fully completing the synthesis is ongoing.
The document discusses solid phase peptide synthesis (SPPS) methods using different protecting groups. It describes the t-Boc and Fmoc protecting group strategies, comparing their advantages and disadvantages. The t-Boc strategy uses acid-labile protecting groups removed by TFA, while the Fmoc strategy uses a base-labile Fmoc group and acid-labile side chain protecting groups, allowing milder acidic conditions. The document outlines the different protocols used in SPPS, including resin attachment, amino acid coupling and protecting group removal steps. It also discusses side reactions that can occur and strategies to minimize them, such as using orthogonal protecting groups or modified amino acid derivatives.
This document discusses peptide synthesis methods, including solution phase peptide synthesis and solid phase peptide synthesis (SPPS). SPPS involves attaching the starting peptide to an inert resin bead and performing sequential amino acid couplings and deprotections while the growing peptide remains attached to the resin. This allows for easy purification after each step. Once the full peptide is synthesized, it is cleaved off the resin bead. SPPS allows for faster synthesis of longer peptides up to 70-100 amino acids in length compared to solution phase synthesis. Applications of synthetic peptides include vaccines, hormones, antibiotics, toxins, and enzyme inhibitors.
Solution And Solid Phase Synthesis Publicationadotse
This document describes the solution- and solid-phase synthesis of peptide-substituted thiazolidinediones as potential ligands for peroxisome proliferator-activated receptors (PPARs). Initial studies focused on the low-yielding solution-phase synthesis of two target compounds. Improved yields were obtained using solid-phase synthesis and protecting the thiazolidinedione nitrogen. A small library of nine resin-bound peptide-substituted thiazolidinediones was then synthesized to examine structural features that facilitate PPAR binding and identify new PPAR activators/inhibitors.
This document discusses the reactions and color tests of amino acids. It describes reactions that can occur due to the amino group, carboxyl group, or both including oxidative deamination, transamination, and peptide bond formation. Reactions involving the side chains of different amino acids like ester formation, disulfide bond formation, and transmethylation are also reviewed. Finally, the document outlines several common color tests used to identify different amino acids including the ninhydrin, biuret, xanthoproteic, Millon's, Sakaguchi, Hopkins Cole, lead acetate, and nitroprusside reactions. The learner will understand the various reactions and color tests used to analyze amino acids.
solid phase synthesis Presentation by komalKomal Rajgire
The document summarizes solid phase synthesis. It begins with an introduction describing how solid phase synthesis involves coupling reagents to a solid support to perform multi-step reactions leading to a target molecule. It then discusses various aspects of planning solid phase synthesis such as suitable resin supports, linkers, protective groups, and monitoring reactions. Examples of resin types, linkers, and protective groups are provided. The document concludes by outlining advantages such as simplified purification and green chemistry principles, as well as disadvantages such as potential low reaction rates. Applications mentioned include combinatorial synthesis, peptide synthesis, and DNA synthesis.
This document discusses strategies for solid phase peptide synthesis (SPPS) using different protecting groups. It compares the t-Boc and Fmoc protection methods, noting the advantages of Fmoc such as using milder acidic conditions for deprotection and cleavage from the resin. Protocols are provided for various steps in Fmoc SPPS including resin loading, amino acid coupling and deprotection, and final cleavage and deprotection. Potential side reactions are also described such as diketopiperazine formation and aspartimide formation, along with ways to prevent these reactions.
CHEMISTRY OF PEPTIDES [M.PHARM, M.SC, BSC, B.PHARM]Shikha Popali
THE CHEMISTRY OF PEPTIDES THE DIFFICULT TO COLLECT DATA FOR READERS , THREFORE HERE WE HAVE COLLECTED ALL THE DATA AT A PLACE AND PROVIDED EASIER TO CHEMISTRIANS.
comprehensive presentation on Detoxification of xenobiotics in human body.This presentation is designed for undergraduate medical ,dental ,biotechnology & pharmacology students for self study.Presentation has Definition of detoxification , classification of toxic substances .Detoxification of endogenous & exogenous toxic substances along with molecular mechanism involved is presented here.Metabolism of xenobiotic (detoxification)
by oxidation. reduction , hydrolysis& conjugation is illustrated with suitable examples.Characteristics of cytochrome P450& its mode of action are described.Google images are used to support the text for better understanding.
The document discusses biotransformation and detoxification reactions. It describes how xenobiotics are metabolized in two phases: Phase 1 involves reactions like hydroxylation and Phase 2 involves conjugating these products to make them more hydrophilic and excretable, through glucuronidation, sulfation, acetylation, methylation or conjugation to amino acids or glutathione. The cytochrome P450 system is important for Phase 1 reactions like oxidation. Phase 2 makes compounds more polar through conjugating them to compounds like glucuronic acid. This allows xenobiotics to be safely eliminated from the body.
Chemistry of peptide (BPHARM,MPHARM,MSC,BSC)Shikha Popali
THE PRESENTATION DESCRIBING BOND FORMATION OF AMINO ACIDS AND PROTEINS AND COUPLING REAGENTS IN PEPTIDE SYNTHESIS FOLLOWED BY CARBODIMIDES, PHOSPHONIUM AND AMMONIUM SALTS.
This document discusses the properties and characteristics of amino acids. It covers their ionic properties, isoelectric points, optical activity, solubility, UV absorption, and various chemical reactions including esterification, acylation, alkylation, reactions with carbonyl compounds, and reactions involving functional groups like cysteine and methionine. It notes that amino acids are important in developing flavors and aromas in foods during high-temperature cooking methods like frying and baking.
This document summarizes the non-mevalonate pathway for isoprenoid biosynthesis. It notes that plants, protozoa like malaria parasites, and most bacteria use this alternative pathway located in their plastids to produce isoprenoids. The pathway converts pyruvate and glyceraldehyde 3-phosphate into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) through a series of enzymatic reactions. Inhibitors of 1-deoxy-D-xylulose 5-phosphate reductoisomerase, a key enzyme in this pathway, like fosmidomycin and its derivative FR-900098, show potential as new
This document discusses protein reactions that occur during food processing. It covers both enzyme-catalyzed and chemical reactions that proteins undergo, including proteolytic enzymes like serine and cysteine endopeptidases. Specific modifications are described, such as the Maillard reaction and changes induced by heat, pH, oxidation. Controlling these reactions through processing conditions and enzymes is important for food properties and safety.
This document provides an overview of basic metabolic pathways in plants. It discusses primary and secondary metabolism, the role of enzymes and co-enzymes, and several key pathways such as the shikimic acid, acetate, and mevalonate pathways. Primary metabolites such as starch, cellulose, and chlorophyll are synthesized through basic metabolic pathways and are essential for plant growth and function. Secondary metabolites are derived from primary metabolites and have pharmacological activities. Enzymes help catalyze biochemical reactions in metabolic pathways, while co-enzymes assist enzymes and participate in reactions. Biosynthesis converts carbon dioxide into carbohydrates through photosynthesis.
This document describes the synthesis of distearoyl-L-(α-glycerylphosphoryl)-N,N-dimethyl-ethanolamine, an N,N-dimethylcephalins. The synthesis involves a multi-step process beginning with glycerylphosphorylcholine and converting it through intermediates to the final product. The goal was to synthesize a reference compound to help elucidate the structure of naturally occurring N-methyl-substituted cephalins and to use as substrates for biological investigations. Details of the experimental procedure and rationale for substrate selection are provided.
A presentation discussing amino acids, peptide bonds and peptide synthesis. The Merrifield Synthesis of Peptides is further discussed covering principle, methodology, isolation and purification, its advantages and disadvantages. A brief note on protecting groups is mentioned. A few practical applications of synthetic peptides are mentioned and discussed in brief as well.
This article discusses how methanol (MeOH) affects ascorbate (AsA) levels and related gene expression in Oncidium orchids. The study found that a low concentration of MeOH (50 mM) triggered hydrogen peroxide (H2O2) production and increased expression of AsA biosynthesis genes. However, a high MeOH concentration was toxic and depleted AsA levels. The increased gene expression from low MeOH levels was blocked by inhibitors of alcohol oxidase and NADPH oxidase, suggesting H2O2 is a signaling molecule regulating AsA gene expression in response to MeOH. The results help explain the mechanism by which MeOH stimulates AsA production in Oncidium at the molecular level.
This document discusses the metabolism of xenobiotics, or foreign compounds, in the body. It describes how xenobiotics undergo two phase biotransformation reactions, with phase 1 involving oxidation, reduction, and hydrolysis, and phase 2 involving conjugation to make compounds more water soluble for excretion. The liver plays a key role in these metabolic reactions through cytochrome P450 enzymes and conjugation enzymes. The document also discusses how reactive oxygen species are generated and the antioxidant systems that help prevent cellular damage from free radicals.
The document summarizes various processes involved in drug biotransformation and elimination from the body. It discusses two main phases - Phase I reactions which involve oxidation, reduction and hydrolysis to make drugs more polar. Phase II reactions then conjugate these products to endogenous moieties like glucuronic acid, sulfate or glutathione to facilitate excretion. Specific reactions in each phase like aromatic hydroxylation, carbonyl reduction, glucuronidation and acetylation are explained in detail.
This document provides an overview of peptides. It defines peptides as short chains of amino acids linked by peptide bonds. Peptides are distinguished from proteins based on their smaller size, typically containing fewer than 50 amino acid units. The document discusses peptide bond formation, characteristics of peptide bonds, classes of peptides, physical properties, examples of individual peptides, food-derived peptides with biological activity, and applications of peptides in molecular biology.
This document discusses a 5 stage structure that has been completed and recommends using the narrative of a short film to list the number of something, and applying Volger's 12 steps to the short film.
Solution And Solid Phase Synthesis Publicationadotse
This document describes the solution- and solid-phase synthesis of peptide-substituted thiazolidinediones as potential ligands for peroxisome proliferator-activated receptors (PPARs). Initial studies focused on the low-yielding solution-phase synthesis of two target compounds. Improved yields were obtained using solid-phase synthesis and protecting the thiazolidinedione nitrogen. A small library of nine resin-bound peptide-substituted thiazolidinediones was then synthesized to examine structural features that facilitate PPAR binding and identify new PPAR activators/inhibitors.
This document discusses the reactions and color tests of amino acids. It describes reactions that can occur due to the amino group, carboxyl group, or both including oxidative deamination, transamination, and peptide bond formation. Reactions involving the side chains of different amino acids like ester formation, disulfide bond formation, and transmethylation are also reviewed. Finally, the document outlines several common color tests used to identify different amino acids including the ninhydrin, biuret, xanthoproteic, Millon's, Sakaguchi, Hopkins Cole, lead acetate, and nitroprusside reactions. The learner will understand the various reactions and color tests used to analyze amino acids.
solid phase synthesis Presentation by komalKomal Rajgire
The document summarizes solid phase synthesis. It begins with an introduction describing how solid phase synthesis involves coupling reagents to a solid support to perform multi-step reactions leading to a target molecule. It then discusses various aspects of planning solid phase synthesis such as suitable resin supports, linkers, protective groups, and monitoring reactions. Examples of resin types, linkers, and protective groups are provided. The document concludes by outlining advantages such as simplified purification and green chemistry principles, as well as disadvantages such as potential low reaction rates. Applications mentioned include combinatorial synthesis, peptide synthesis, and DNA synthesis.
This document discusses strategies for solid phase peptide synthesis (SPPS) using different protecting groups. It compares the t-Boc and Fmoc protection methods, noting the advantages of Fmoc such as using milder acidic conditions for deprotection and cleavage from the resin. Protocols are provided for various steps in Fmoc SPPS including resin loading, amino acid coupling and deprotection, and final cleavage and deprotection. Potential side reactions are also described such as diketopiperazine formation and aspartimide formation, along with ways to prevent these reactions.
CHEMISTRY OF PEPTIDES [M.PHARM, M.SC, BSC, B.PHARM]Shikha Popali
THE CHEMISTRY OF PEPTIDES THE DIFFICULT TO COLLECT DATA FOR READERS , THREFORE HERE WE HAVE COLLECTED ALL THE DATA AT A PLACE AND PROVIDED EASIER TO CHEMISTRIANS.
comprehensive presentation on Detoxification of xenobiotics in human body.This presentation is designed for undergraduate medical ,dental ,biotechnology & pharmacology students for self study.Presentation has Definition of detoxification , classification of toxic substances .Detoxification of endogenous & exogenous toxic substances along with molecular mechanism involved is presented here.Metabolism of xenobiotic (detoxification)
by oxidation. reduction , hydrolysis& conjugation is illustrated with suitable examples.Characteristics of cytochrome P450& its mode of action are described.Google images are used to support the text for better understanding.
The document discusses biotransformation and detoxification reactions. It describes how xenobiotics are metabolized in two phases: Phase 1 involves reactions like hydroxylation and Phase 2 involves conjugating these products to make them more hydrophilic and excretable, through glucuronidation, sulfation, acetylation, methylation or conjugation to amino acids or glutathione. The cytochrome P450 system is important for Phase 1 reactions like oxidation. Phase 2 makes compounds more polar through conjugating them to compounds like glucuronic acid. This allows xenobiotics to be safely eliminated from the body.
Chemistry of peptide (BPHARM,MPHARM,MSC,BSC)Shikha Popali
THE PRESENTATION DESCRIBING BOND FORMATION OF AMINO ACIDS AND PROTEINS AND COUPLING REAGENTS IN PEPTIDE SYNTHESIS FOLLOWED BY CARBODIMIDES, PHOSPHONIUM AND AMMONIUM SALTS.
This document discusses the properties and characteristics of amino acids. It covers their ionic properties, isoelectric points, optical activity, solubility, UV absorption, and various chemical reactions including esterification, acylation, alkylation, reactions with carbonyl compounds, and reactions involving functional groups like cysteine and methionine. It notes that amino acids are important in developing flavors and aromas in foods during high-temperature cooking methods like frying and baking.
This document summarizes the non-mevalonate pathway for isoprenoid biosynthesis. It notes that plants, protozoa like malaria parasites, and most bacteria use this alternative pathway located in their plastids to produce isoprenoids. The pathway converts pyruvate and glyceraldehyde 3-phosphate into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) through a series of enzymatic reactions. Inhibitors of 1-deoxy-D-xylulose 5-phosphate reductoisomerase, a key enzyme in this pathway, like fosmidomycin and its derivative FR-900098, show potential as new
This document discusses protein reactions that occur during food processing. It covers both enzyme-catalyzed and chemical reactions that proteins undergo, including proteolytic enzymes like serine and cysteine endopeptidases. Specific modifications are described, such as the Maillard reaction and changes induced by heat, pH, oxidation. Controlling these reactions through processing conditions and enzymes is important for food properties and safety.
This document provides an overview of basic metabolic pathways in plants. It discusses primary and secondary metabolism, the role of enzymes and co-enzymes, and several key pathways such as the shikimic acid, acetate, and mevalonate pathways. Primary metabolites such as starch, cellulose, and chlorophyll are synthesized through basic metabolic pathways and are essential for plant growth and function. Secondary metabolites are derived from primary metabolites and have pharmacological activities. Enzymes help catalyze biochemical reactions in metabolic pathways, while co-enzymes assist enzymes and participate in reactions. Biosynthesis converts carbon dioxide into carbohydrates through photosynthesis.
This document describes the synthesis of distearoyl-L-(α-glycerylphosphoryl)-N,N-dimethyl-ethanolamine, an N,N-dimethylcephalins. The synthesis involves a multi-step process beginning with glycerylphosphorylcholine and converting it through intermediates to the final product. The goal was to synthesize a reference compound to help elucidate the structure of naturally occurring N-methyl-substituted cephalins and to use as substrates for biological investigations. Details of the experimental procedure and rationale for substrate selection are provided.
A presentation discussing amino acids, peptide bonds and peptide synthesis. The Merrifield Synthesis of Peptides is further discussed covering principle, methodology, isolation and purification, its advantages and disadvantages. A brief note on protecting groups is mentioned. A few practical applications of synthetic peptides are mentioned and discussed in brief as well.
This article discusses how methanol (MeOH) affects ascorbate (AsA) levels and related gene expression in Oncidium orchids. The study found that a low concentration of MeOH (50 mM) triggered hydrogen peroxide (H2O2) production and increased expression of AsA biosynthesis genes. However, a high MeOH concentration was toxic and depleted AsA levels. The increased gene expression from low MeOH levels was blocked by inhibitors of alcohol oxidase and NADPH oxidase, suggesting H2O2 is a signaling molecule regulating AsA gene expression in response to MeOH. The results help explain the mechanism by which MeOH stimulates AsA production in Oncidium at the molecular level.
This document discusses the metabolism of xenobiotics, or foreign compounds, in the body. It describes how xenobiotics undergo two phase biotransformation reactions, with phase 1 involving oxidation, reduction, and hydrolysis, and phase 2 involving conjugation to make compounds more water soluble for excretion. The liver plays a key role in these metabolic reactions through cytochrome P450 enzymes and conjugation enzymes. The document also discusses how reactive oxygen species are generated and the antioxidant systems that help prevent cellular damage from free radicals.
The document summarizes various processes involved in drug biotransformation and elimination from the body. It discusses two main phases - Phase I reactions which involve oxidation, reduction and hydrolysis to make drugs more polar. Phase II reactions then conjugate these products to endogenous moieties like glucuronic acid, sulfate or glutathione to facilitate excretion. Specific reactions in each phase like aromatic hydroxylation, carbonyl reduction, glucuronidation and acetylation are explained in detail.
This document provides an overview of peptides. It defines peptides as short chains of amino acids linked by peptide bonds. Peptides are distinguished from proteins based on their smaller size, typically containing fewer than 50 amino acid units. The document discusses peptide bond formation, characteristics of peptide bonds, classes of peptides, physical properties, examples of individual peptides, food-derived peptides with biological activity, and applications of peptides in molecular biology.
This document discusses a 5 stage structure that has been completed and recommends using the narrative of a short film to list the number of something, and applying Volger's 12 steps to the short film.
This document summarizes Ebba Ossiannilsson's presentation on MOOCs and quality. The presentation discusses the rise of MOOCs and their key characteristics of being massive, open, online courses. It also examines students, support, content, and recommendations from the European Commission around opening up education through digital technologies and MOOCs. Quality factors for MOOCs discussed include ensuring a framework for openness, learner-centeredness, independent learning, and media support. The presentation promotes the MOOC Quality Project and label of OpenupEd and provides contact information for Ebba Ossiannilsson.
This document summarizes an OER higher education meeting focused on quality. It includes notes from presentations by Ebba Ossiannilsson of Lund University, Sweden on her dissertation research on benchmarking e-learning and comments from a 2012 EADTU conference. Key points covered include definitions of open educational resources and the Paris Declaration principles of OER including awareness, enabling environments, strategies, open licensing, and quality. Recommendations are made around exploiting MOOCs, innovative practices, digital skills, validating online learning, and accessing high quality open resources. Emergent themes discussed shifting to open practices using social media to foster communities.
Ossiannilsson 131024 eadtu Presentation on disstance students attitudes to th...Ebba Ossiannilsson
EADTU annual Conference24-25 October 2013. My presentation on Students attitudes to distance education at Lund University, SE based on Statistics Swedens survey on distance students attitudes on their education
The document is a shot list template for a film or video production. It includes directions for different camera shots including extreme close-up, close-up, and wide shot. It also includes directions for camera movements like panning and tilting. For each shot, the template includes the type of shot, the subject that will be filmed, and the action that will occur. Contact information is provided for any questions.
The document discusses trends in open and collaborative learning including massive open online courses (MOOCs) and open educational resources (OER). It notes that higher education is key to a skilled workforce and a strong economy. However, outdated educational models limit students' ability to learn anywhere and participate successfully in modern society. The document advocates opening up education through digital technologies to support learning anywhere, anytime through any device. It also discusses barriers to open learning cultures and the importance of skills like filtering, curating and collaborating in personal learning environments and communities of practice.
Open & Shut: Leadership in the Social WorldJordan Epp
This document discusses the current climate of social technologies and expectations for leadership. It notes major shifts from industrial to information age models and from systems-based to networked approaches. Open leadership is described as happening online and offline, focusing on participation, sharing, and building community. Skills for open leadership include technical proficiency, digital communication, content curation, and netiquette like transparency and authenticity. The concept of legitimate peripheral participation in online communities is also referenced.
Technological convergence refers to the integration of telecommunications, information technology, and media sectors that were originally separate. It presents both opportunities and challenges. Key opportunities include increased market competition through lower barriers to entry, new services and applications, and convenience through multifunction devices. However, convergence also poses challenges such as developing new regulatory frameworks, upgrading infrastructure to support bandwidth-intensive new services, strategic realignment for operators and providers, and ensuring security, privacy and reliability with increased network complexity. Overall, convergence offers potential for new value-added services and expanded markets if these challenges are adequately addressed.
The document discusses how digital technologies and online learning are transforming education for the "Y generation" in the digital age. Key points discussed include the increasing importance of skills like digital literacy, mobility and ubiquitous learning, networking and collaboration over traditional content consumption, and the growing role of learners as self-directed "backpack learners" who can access education resources from anywhere through open online courses and networks. Recommendations from the European Commission emphasize exploiting technologies like MOOCs, equipping teachers and learners with digital skills, and transforming education systems to be more open, flexible and lifelong.
The document repeats various interrogative pronouns and adverbs with no discernible meaning or story. It briefly mentions Victor sitting on a fence and Arna lying in bed and liking TV and bed, except for a TV program, and then going outside while Victor ate a camera.
This document discusses quality assurance (QA) in e-learning and the E-xcellence instrument launched in 2007 to complement existing internal and external QA systems. The basic tool in E-xcellence is the quick scan, which can be done as a quick orientation, with a review at a distance, or with an on-site assessment. It aims to reward continuous educational improvement through the E-xcellence Associates label. QA agencies and universities need to cooperate on e-learning QA and work towards a common definition and understanding of e-learning standards. The SEQUENT project also aims to promote excellence in ICT use in higher education and prepare universities for cross-border collaboration.
The document discusses quality development of e-learning and online learning for the 180 credit occupational therapist program at Luleå University of Technology. It provides information on the program being a distance education program with skills training and laboratory work on campus. It discusses communication tools used like Fronter and Adobe Connect Pro. It also outlines drivers of change in education like technology, globalization, and labor market trends. Key aspects of quality in e-learning are discussed including learning design, media design, and evaluation. Benchmarking of e-learning is presented as a process to improve performance by learning from other institutions.
The document lists the top 10 lessons learned from successful New York City entrepreneurs. It provides short quotes from entrepreneurs such as Kenny Dichter of Marquis Jet on the power of partnerships, Gretchen Shugart of Theatermania.com on partnerships that make sense, and Brandon Steiner of Steiner Sports on helping customers instead of just selling. Other lessons mentioned include trying before you buy, not listening to naysayers, staying in touch with customers, hiring inexperienced people, recognizing mistakes early, managing frustration, and prioritizing employees before customers.
This document provides an overview of using the version control system GIT for TYPO3 development. It discusses key GIT concepts and commands for creating repositories, branching, merging, resolving conflicts, and collaborating remotely. The agenda also covers file exclusion, changing commits, interactive adding, stashing, rebasing, and interoperability with SVN repositories.
1. Paracetamol is generally safe at recommended doses but can cause acute liver failure and require transplantation at higher overdose doses due to its intrinsic toxicity.
2. At therapeutic doses, paracetamol is mainly metabolized through non-toxic pathways like sulfation and glucuronidation. However, at overdose levels it is oxidized by cytochrome P450 2E1 to form the toxic metabolite NAPQI.
3. NAPQI is normally detoxified by conjugating with glutathione, but an overdose depletes glutathione reserves allowing NAPQI to accumulate and cause
Plants have evolved chemical defenses like proteinase inhibitors and toxic compounds to protect themselves from damage. Jasmonic acid (JA) is a key signaling compound that induces these defenses. JA is synthesized from linolenic acid through the octadecanoid pathway. It regulates processes like growth, photosynthesis, and defense. JA signaling involves peptide signals like systemin and leads to both local and systemic responses in plants.
This document is a research project report submitted by Rebecca Holmes in partial fulfillment of a BSc in Biochemistry. The report investigates the alkene monooxygenase enzyme from Rhodococcus rhodochrous B-276 which is able to catalyze the stereoselective epoxidation of terminal and subterminal alkenes. Genomic DNA extraction and sequencing was conducted to identify the bacterial strain. SDS-PAGE analysis was unable to detect proteins, suggesting extraction methods need improvement. Propene oxidation assays using different preparation techniques were analyzed by gas chromatography, detecting propene but not epoxypropane. Further research into oxidizing other alkenes using freshly cultured cells could provide valuable chiral epox
Plant responses to oxidative stress can cause physiological damage at the lipid, protein, and DNA levels. Physiologically, lipid peroxidation disrupts cell membranes, protein oxidation alters structure and function, and DNA oxidation causes mutations. Biochemically, plants have developed defense mechanisms including superoxide dismutase, catalase, peroxidase, and glutathione to neutralize reactive oxygen species. Glutathione functions in redox reactions and membrane stabilization. Plants also produce antioxidants like carotenoids to counteract oxidative stress and protect cellular components from free radical damage.
The document discusses taxadiene-4(5)-epoxide (12), a potential intermediate in the taxol biosynthetic pathway. The authors:
1) Show for the first time that taxadiene can be selectively epoxidized to form taxadiene-4(5)-epoxide (12) and that this epoxide can rearrange to taxa-4(20),11(12)-dien-5a-ol (4).
2) Find that unlike previous speculation, epoxide 12 can rearrange when exposed to iron(III) porphyrin, supporting consideration of it as a chemically competent intermediate.
3) Suggest their observations justify re
This document describes the efficient synthesis of glaziovianin A (GVA) and related isoflavones starting from readily available plant metabolites. A six-step reaction sequence involving bromination, alkylation, oxidation, condensation, epoxidation, and cyclization produced GVA and various alkoxyphenyl derivatives. Both an in vivo sea urchin embryo assay and screening of human cancer cell lines showed that GVA and some derivatives have antimitotic effects by destabilizing microtubules. Structure-activity relationship studies found that certain substituents, such as a methylenedioxy or trimethoxy group, influenced the compounds' potency. GVA was generally the most active compound, inhibiting cancer cell
This document summarizes key information about eicosanoids, isoprenoids, terpenes, and steroids. It discusses the structures and classifications of these lipid derivatives. Key points include: Eicosanoids are C20 fatty acid derivatives that act as local hormones. There are two major types: cyclic prostanoids and acyclic leukotrienes/lipoxins. Prostaglandins and thromboxanes are examples of prostanoids. Isoprenoids are composed of isoprene units and include terpenes found in plants. Terpenes are classified based on the number of isoprene units. Steroids are derived from squalene and cholesterol, and include hormones like progesterone,
1) Chiral phosphoric acid catalyst PA-1 promotes the highly enantioselective ring-opening of meso-aziridines with a variety of functionalized aromatic thiols. The reaction proceeds in good yields and up to 97% enantiomeric excess without requiring silylated thiol nucleophiles.
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This document summarizes different classes of lipids, including eicosanoids, terpenoids, steroids, and phytosterols. It describes the structures and properties of prostaglandins, leukotrienes, lipoxins, terpenes, carotenoids, dolichol, coenzyme Q, cholesterol, bile acids, phytosterols like sitosterol and stigmasterol. Examples are provided of monoterpenes, sesquiterpenes, diterpenes, and tetraterpenes. The roles of these lipids in biological processes and potential applications are briefly mentioned.
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Denis is a dynamic and results-driven Chief Information Officer (CIO) with a distinguished career spanning information systems analysis and technical project management. With a proven track record of spearheading the design and delivery of cutting-edge Information Management solutions, he has consistently elevated business operations, streamlined reporting functions, and maximized process efficiency.
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Date: May 29, 2024
Tags: Information Security, ISO/IEC 27001, ISO/IEC 42001, Artificial Intelligence, GDPR
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Temple of Asclepius in Thrace. Excavation resultsKrassimira Luka
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2008 molecular mechanism of enzymatic allene oxide cyclization in plants
1. Available online at www.sciencedirect.com
Plant Physiology and Biochemistry 46 (2008) 302e308
www.elsevier.com/locate/plaphy
Review
Molecular mechanism of enzymatic allene oxide cyclization in plants
Eckhard Hofmann a,*, Stephan Pollmann b
a
Biophysics, Department of Biology and Biotechnology, Ruhr-University Bochum, Universitaetsstrasse 150, D-44801 Bochum, Germany
b
Plant Physiology, Department of Biology and Biotechnology, Ruhr-University Bochum, Universitaetsstrasse 150, D-44801 Bochum, Germany
Received 14 November 2007
Available online 31 December 2007
Abstract
Jasmonates, a collective term combining both jasmonic acid (JA) and related derivatives, are ubiquitously distributed in the plant kingdom.
They are characterized as lipid-derived signal molecules which mediate a plethora of physiological functions, in particular stress responses, male
fertility, and a multitude of developmental processes. In the course of JA biosynthesis, the first oxylipin with signal character, cis-(þ)-12-oxo-
phytodienoic acid (OPDA), is produced in a cyclization reaction catalyzed by allene oxide cyclase (AOC). This enzyme-catalyzed ring closure is
of particular importance, as it warrants the enantiomeric structure at the cyclopentenone ring which in the end results in the only bioactive JA
enantiomer, cis-(þ)-JA. In this review, we focus on the structural and molecular mechanisms underlying the above mentioned cyclization re-
action. In this context, we will discuss the crystal structure of AOC2 of Arabidopsis thaliana with respect to putative binding sites of the instable
substrate, 12,13-epoxy-9(Z ),11,15(Z )-octadecatrienoic acid (12,13-EOT), as well as possible intermolecular rearrangements during the cycliza-
tion reaction.
Ó 2007 Elsevier Masson SAS. All rights reserved.
Keywords: Allene oxide cyclase; Allene oxide synthase; Jasmonate; 12-Oxo-phytodienoic acid; Oxylipins; X-ray structure
1. Introduction Jasminum grandiflorum in the early 1960s [7], it took nearly
another twenty years until the first physiological effects of
Besides brassinosteroids and oligopeptides with hormone- MeJA and the occurrence of the free acid were described
like functions, the jasmonates are among the most recently [4,33]. To date, jasmonic acid and its derivatives are associated
identified signal molecules with phytohormone properties, with diverse physiological functions. The most prominent one
and are widespread throughout a variety of different plant is the involvement of JA in wound response and pathogenesis
phyla [25]. Although the jasmonic acid methyl ester (MeJA) [8,18,37]. Additionally, jasmonates play a crucial role in re-
was demonstrated to be a constituent of the essential oil of production [9], metabolic regulation [35], and as a signal
transducer in mechanotransduction [31,38,39]. JA is also re-
quired for protection from ozone damage [26,27], and has
Abbreviations: ACS, acyl-CoA synthase; AOC, allene oxide cyclase; 12,13- a pivotal role in the production of protective secondary metab-
EOT, 12,13(S )-epoxy-9(Z ),11,15(Z )-octadecatrienoic acid; 12,13-EOD, olites in cell cultures of Eschscholtzia californica [2,3].
12,13(S )-epoxy-9(Z ),11-octadecatrienoic acid; AOS, allene oxide synthase; The pathway of jasmonic acid biosynthesis is shown in
CESG, Center for Eucaryotic Structural Genomics; CTS/PXA1, ABC trans-
porter for OPDA or OPDA-CoA import; HPOD, 13(S )-hydroperoxy-
Fig. 1. Jasmonic acid and its octadecanoid precursors are syn-
9(Z ),11(E )-octadecadienoic acid; JA, jasmonic acid; MeJA, jasmonic acid thesized from a-linolenic acid (a-LA) which is found in great
methylester; OPC-8:0, 3-oxo-2(20 (Z )-pentenyl)-cyclopentane-1-octanoic acid; extent in plastidial membranes. From there, a-LA is suggested
LA, a-linolenic acid; OPDA, 12-oxo-phytodienoic acid; OPR, 12-oxo-phytodie- to be released by the action of lipases, e.g. the phospholipase
noic acid reductase; 13(S )-HPOT, 13(S )-hydroperoxy-9(Z ),11(E ),15(Z )-octa- A1 DAD1 [19]. The subsequent oxygenation of a-LA at the
decatrienoic acid; 13-LOX, 13-lipoxygenase.
* Corresponding author. Tel.: þ49 234 32 24463; fax: þ49 234 32 14238.
C-13 position is catalyzed by 13-lipoxygenase [1]. The resulting
E-mail address: eckhard.hofmann@bph.ruhr-uni-bochum.de (E. 13-hydroperoxide, 13(S )-hydroperoxy-9(Z ),11(E ),15(Z )-
Hofmann). octadecatrienoic acid (13-HPOT), is further dehydrated with
0981-9428/$ - see front matter Ó 2007 Elsevier Masson SAS. All rights reserved.
doi:10.1016/j.plaphy.2007.12.007
2. E. Hofmann, S. Pollmann / Plant Physiology and Biochemistry 46 (2008) 302e308 303
the help of allene oxide synthase [29,30], providing the unstable
intermediate, 12,13-epoxy-9(Z ),11,15(Z )-octadecatrienoic
acid (12,13-EOT). Allene oxide cyclase [14,32] catalyzes the
reaction within the octadecanoid pathway which guarantees
enantiomeric specificity, by converting 12,13-EOT to 12-
oxo-10,15(Z )-phytodienoic acid (OPDA). OPDA is then trans-
ferred from the chloroplast to the peroxisome where it is further
metabolized by reduction of the D10-double bond catalyzed
by oxo-phytodienoic acid reductase [28], yielding 3-
oxo-2(20 (Z )-pentenyl)-cyclopentane-1-octanoic acid (OPC-
8:0). Due to radiotracer experiments [36], it is generally agreed
that OPC-8:0 undergoes three consecutive cycles of b-oxidation
which results in the production of bioactive JA with (3R,7S )-
configuration, i.e. (þ)-7-iso-JA.
Allene oxide cyclase (AOC) has been described for the first
time from Zea mays [14,41], followed by the cloning of the
corresponding genes from tomato [42], Arabidopsis [32], and
barley [24]. While in tomato AOC is encoded as a single
gene, in A. thaliana four isogenes can be found, which most
likely evolved from one ancestral isoform by gene duplication
events. With respect to functional differences of the four isoen-
zymes, it has been shown that especially AOC2 mRNA accumu-
lates in the case of local as well as systemic wound response,
whereas AOC1 mRNA seems to be preferentially transcribed
in systemic wound response. By reason that allene oxide syn-
thase (AOS) transcription is also systemically induced after
wounding [20,21], a specific interaction of AOS and AOC1
might be supposable in systemically responding leaves. Further
evidence for functional differences of the AOCs is emphasized
by the occurrence of dinor-oxo-phytodienoic acid (dnOPDA)
which is synthesized from hexadecatrienoic acid. Possibly,
in this context, the isoenzymes possess diverse substrate
specificities [32]. Unfortunately, investigations of either en-
zyme kinetic or substrate specificity of the AOCs have been
hampered by the instability of their substrate. So far, all activity
assays utilized a coupled test system, determining the combined
activity of both AOS and AOC.
The AOCs from Arabidopsis contain a predicted plastidial
target sequence which facilitates the import of the enzymes
into the chloroplast. Functional import of AOC into the chloro-
plast, investigated by immunocytochemical means, has already
been described [32]. However, differentiation between the indi-
vidual isoforms was not possible, suggesting that a more de-
tailed examination of the import of the single isoforms of
AOC is needed. Intriguingly, the expression of Arabidopsis
AOCs has been shown for all plant organs, including roots
[6]. This finding is in contrast to that obtained from tomato
where AOC expression is described to be restricted to floral
Fig. 1. Pathway of jasmonic acid biosynthesis in plants. Intermediates are ab- organs and vascular bundles [15]. However, there are still
breviated as: 13-HPOT, 13(S )-hydroperoxy-9(Z ),11(E ),15(Z )-octadecatrie-
many open questions which mark challenges for future work.
noic acid; 12,13-EOT, 12,13(S )-epoxy-9(Z ),11,15(Z )-octadecatrienoic acid;
OPDA, cis-(þ)-12-oxo-phytodienoic acid; OPDA-CoA, cis-(þ)-12-oxo-phyto- One of the most urgent topics, after unraveling the molecular
dienoic acid-coenzyme A; OPC8:0, 3-oxo-2(20 (Z )-pentenyl)-cyclopentane-1- mechanism of AOC catalyzed 12,13-EOT cyclization, is the
octanoic acid. The enzymes are indicated as: LIP, lipase; LOX, lipoxygenase; elucidation of the functional interconnection of AOS and
AOS, allene oxide synthase; AOC, allene oxide cyclase; OPR, oxo-phytodie- AOC. Although a covalent interaction of AOS and AOC has
noic acid reductase; CTS/PXA1, comatose, ABC transporter for OPDA or
been described as unnecessary [40], the close vicinity of the
OPDA-CoA import; ACS, acyl-CoA synthase.
two proteins seems to enhance their combined activity
(P. Zerbe, personal communication).
3. 304 E. Hofmann, S. Pollmann / Plant Physiology and Biochemistry 46 (2008) 302e308
2. Structures of AOC2 looking along the threefold axis; in Fig. 3 the monomer is
shown.
The structure of AOC2 from Arabidopsis thaliana has been The main structural feature of AOC2 is the central 8-
determined by X-ray crystallography independently in two stranded antiparallel b-barrel. It has a slightly elliptical cross
different labs. Due to these efforts five different structures ˚
section with axes of about 14 and 18 A and walls of height be-
are available from the protein databank. Selenomethionine tween 11 and 30 A ˚ [16]. The barrel is not filled completely by
labeled protein has been crystallized in orthorhombic space side chain atoms but rather forms an elongated hydrophobic
˚ ˚
groups and solved to a resolution of 1.7 A and 1.5 A by the cavity reaching deep into the protein. Notably the highest re-
Center for Eucaryotic Structural Genomics (CESG) (1Z8K, gions of the wall (strands 3e5) which show the most extended
Wesenberg et al., unpublished) and by a group from the h-bonding network and are therefore expected to be the most
Ruhr University Bochum (2BRJ, [16]), respectively. The inde- stable areas of the structure interact with the neighboring
pendently determined structures superpose extremely well monomers in the trimer interface. This trimerization interface
with an overall root mean square deviation of only 0.31 A ˚ ˚
covers roughly 2000 A2 of a monomer surface [16]. While the
for 173 Ca atoms [16]. In both crystal packings one stable barrel is formed by residues 17e147, the remaining 41 C-
trimer of AOC2 is observed per asymmetric unit. As a control terminal residues (colored salmon in Fig. 3) form a mixture
the Bochum group also solved the structure of the unlabelled of helical and random coil structures, which cover the bottom
˚
protein in a monoclinic spacegroup at 1.8 A with two trimers of the barrel and the sides not involved in trimerization. The
in the asymmetric unit (2GIN, [16]). Of functional importance first 16 N-terminal residues are not visible in the structure
is the result of soaking experiments of orthorhombic crystals due to disorder. They consist of the engineered His6-tag with
with a competitive inhibitor, which led to the coordinates of
this molecule inside the proposed catalytic site of the enzyme
(2DIO, [16]). Reevaluation of the original data of the CESG
with an improved refinement protocol resulted in the deposi-
tion of the fifth coordinate set (2Q4I, [22]).
In the following review we will use the highest resolution
coordinates 2BRJ to introduce the overall architecture of the
enzyme. As noted above, in all crystal forms observed so
far, AOC2 was found to form a trimeric quarternary struc-
ture. In Fig. 2 this trimer is shown in ribbon representation
Fig. 2. Structure of AOC2 from Arabidopsis thaliana. Shown is the complete
trimer found in the asymmetric unit of the crystal (accession code 2BRJ). Each Fig. 3. The AOC2 monomer. Shown is the protein in ribbon representation
monomer is individually colored from blue (N-terminus) to red (C-terminus) (2BRJ, chain A). The C-terminal residues 148e188 are colored in salmon.
and labeled with the chain ID (A,B,C). The position of the threefold non- The view is rotated about 90 with respect to Fig. 2. The b-strands of the barrel
crystallographic axis is marked by the black triangle. Figure produced with are labeled S1eS8, the termini of the model are labeled N and C.
Pymol [5]. Figure produced with Pymol [5].
4. E. Hofmann, S. Pollmann / Plant Physiology and Biochemistry 46 (2008) 302e308 305
some additional linker residues and the first two residues after O O
the predicted signal peptidase processing site. The equivalent
residues are missing in all structures in the database so far, re- O O
gardless of the expression constructs used. O O
12,13-EOT 12,13-EOD
Based on topological arguments and on the results of
a DALI-search [17], AOC has been tentatively assigned to
be a member of the lipocalin family [10,16]. Intriguingly, par-
allels exist both in the overall architecture and the substrate
class bound in the central cavity. Most notably prostaglandin O
D synthase is an enzyme involved in the prostanoid synthesis AOC2
in mammals and has been found to share a lipocalin fold [34]. O
Nevertheless key sequence features of lipocalins [10] are miss-
O
ing in the AOC2 structure and the observed similarity might 12,13-Epoxyoctadecadienoic acid
well be a result of convergent evolution instead of a common
O
ancestor [16]. Based on sequence data, the four other known
O
lipocalins from plants have been classified to be members of
O
a divergent subclass of lipocalins termed outlier lipocalins
[13]. Therefore the proposal should be critically reevaluated OPDA
once more lipocalins from plants are structurally known.
Fig. 4. Structural formulas of productive substrate 12,13-EOT, not cyclizable
The finding that AOC2 forms trimers in the crystal struc- analogs 12,13-EOD and the competitive inhibitor vernolic acid (12,13 epox-
tures led to a reevaluation of biochemical data. For corn yoctadecadienoic acid) together with the product OPDA.
AOC a dimeric form had been proposed based on size exclu-
sion chromatography [41]. Similar results have been reported
for AOC2 [16], but have been interpreted as being compatible distance to the conserved water molecule W75. In the complex
with trimers. The observation of SDS-stable trimers both in structure no induced fit of the protein is observed (Fig. 5A).
plant extracts and in purified enzyme led to the conclusion Based on the structural evidence for the binding of vernolic
that the retardation on the size exclusion column might be acid, both substrate 12,13-EOT and product OPDA were mod-
higher than expected by the molecular weight. A more system- eled into the binding pocket to facilitate discussion of possible
atic biochemical analysis is underway in our laboratory but reaction mechanisms (Fig. 5B) [16]. On this basis the follow-
has not yet resulted in clear evidence for the oligomeric state ing scheme was postulated: 12,13-EOT binds with the u-end
in solution (S. Pollmann, unpublished results). into the hydrophobic pocket of AOC2. The epoxide oxygen
is coordinated by a conserved water molecule, which is in
3. The reaction mechanism turn tightly bound by the surrounding protein residues P32,
S31, N25 and N53. The carboxylic moiety of 12,13-EOT rea-
Analysis of the AOC2 structure already suggests that the ches out of the pocket to the surface of the protein. Cyclization
active site is located inside the barrel cavity. While it is mostly is initiated by the delocalization of the C15 double bond which
lined by hydrophobic and aromatic residues, three patches of in turn is triggered by the essential E23 (Fig. 6A). This leads to
more polar residues are noteworthy. One patch is formed by the epoxide opening by anchimeric assistance. The importance
a proline (P32), serine (S31), and two asparagine residues of the C15 double bond for enzyme-controlled cyclization has
(N25, N53) which coordinate a water molecule found in all been demonstrated by several studies and would be rational-
available AOC structures so far. On the opposite side of the ized by this proposal. After epoxide opening the resulting oxy-
barrel wall a cysteine (C71) is located. Finally at the bottom anion is readily stabilized by the conserved water. Hofmann
of the barrel a glutamate residue (E23) is found. All of these et al. [16] proposed the formation of a classical pentadienyl
residues are strictly conserved in known AOC sequences. cation. To reach a productive conformation a transecis isom-
To obtain experimental evidence for the location of the ac- erization around the C10eC11 bond has to be assumed, which
tive site the competitive inhibitor vernolic acid has been used could be driven by the hydrophobic effect due to a better burial
(Fig. 4). It differs from the substrate EOT by the absence of the of the hydrocarbon chain in the pocket. The resulting non-
C11eC12 double bond and can therefore not undergo the cy- planar dienyl-like pentadienyl cation would be stabilized by
clization reaction. Vernolic acid has been shown to be a potent pep interactions of nearby aromatic residues; also the con-
inhibitor of the corn AOC [41], but the inhibitory effect is not served C71 was postulated to stabilize the delocalized positive
as pronounced in the case of Arabidopsis AOC1-4 (P. Zerbe, charge (Fig. 6B). The final step of the reaction would be a con-
personal communication). rotary pericyclic ring closure along the lines of the Wood-
In the structure of AOC2 in complex with vernolic acid wardeHoffmann rules (Fig. 6C). Stereoselectivity would be
(2DIO; Fig. 5A), the inhibitor is bound with the acyl chain mainly achieved by the geometrical control of the transecis
buried deep inside the pocket. The carboxylic moiety is not isomerization by the hydrophobic parts of the pocket.
tightly bound, but rather flexible on the protein surface. The While the proposed mechanism builds upon the concept of
epoxy group of vernolic acid is found in hydrogen-bonding anchimeric assistance proposed for the oxylipin cyclization by
5. 306 E. Hofmann, S. Pollmann / Plant Physiology and Biochemistry 46 (2008) 302e308
Fig. 5. The AOC2 binding pocket. (A) Inhibitor vernolic acid (VA, salmon stick model) bound in the barrel cavity. Shown are both the ligand-free (2BRJ, grey) and
˚
the ligand-bound (2DIO, yellow) structure superposed. Residues closer than 4 A to either vernolic acid or the conserved water molecule W75 (red sphere) are
shown as sticks. (B) Substrate EOT (green) and reaction product OPDA (purple) modeled into the binding pocket of AOC2. The conserved water molecule
W75 is shown as a red sphere, surrounding sidechains are shown as sticks and labeled. Figure produced with Pymol [5].
Grechkin and coworkers [11], and assumes therefore a similar 4. Comparison with other AOC structures
reaction initiation, it differs in the assumed mechanism for
ring closure. In solution a strong dependency of the cyclization A new structure of AOC2 has been deposited recently by the
reaction of 12,13-EOT on the pH has been observed [12], CESG (2Q4I, [22]). Here the original crystallographic data
which cannot be easily explained by a classical pericyclic have been reevaluated with an ensemble refinement method.
ring closure. Instead Grechkin et al. [12] propose a dipolar an- AOC2 has been one of 50 structures used in this methodolog-
nulation mechanism, which includes an intermediate with ical study and is not separately discussed in the paper. In the
a carbanion located at C-9 and a carbocation located at C- deposited coordinates 8 different conformers have been refined
13. This concept is needed to accommodate the observed in parallel to allow a better representation of the inherent
pH-dependency and has been generally accepted. flexibility in the protein. The rationale behind the method is
For the enzyme-controlled reaction the situation is slightly the observation that this kind of model fits the experimental
different. In the rather tight hydrophobic pocket no free sol- data better and should therefore be more informative than the
vent molecules are available to act as stabilizing counter- classical model with isotropic temperature factors for single
charges for intermediate ionic states in the course of the atoms modeling the inherent disorder. Discussion of this ap-
reaction. Instead stabilization has to be facilitated by protein proach is beyond the scope of this review, but a brief analysis
side chains or tightly bound water molecules. So far the of the ensemble model confirms the rigid nature of the barrel,
structural evidence does not present a likely candidate to sta- while the exterior loops show a somewhat higher flexibility.
bilize the proposed carbanion localized at C-9. Therefore the Most notably the backbone and side chains of residues around
more classical scheme with a delocalized charged intermedi- the active site do not show any significant shifts in the different
ate seems to be more favorable. In addition the scheme members of the ensemble.
would be in agreement with a theoretical study on vinyl In the target list of the CESG all four isoforms of AOC have
allene oxides, suggesting a stepwise mechanism including been included (http://targetdb.pdb.org/). In addition to the
strong enantiofacial torque selectivity enforced by the protein structures of AOC2 mentioned above, the structure of AOC1
[23]. ˚
has also been solved at a resolution of 1.8 A and deposited in
Nevertheless, one has to bear in mind that there is no real the PDB (1ZVC). Interestingly, AOC1 also crystallizes as a tri-
structure of the substrateeenzyme complex, which might mer, but in a completely different crystallographic environ-
well show detailed structural features in favor of the annula- ment. This supports the hypothesis of the trimer being
tion mechanism. In addition analysis of point mutations in a relevant aggregation state of AOC1 and AOC2 in vivo. A
the active site area might allow discrimination between the comparison between the two structures showed no significant
two concepts and will clarify the situation. Clearly, more structural deviations [16]. Both proteins are very similar and
work is needed for a full understanding of the reaction differ only in 10 positions in sequence, most of which represent
mechanism. conservative changes (Fig. 7). None of these mutations are
6. E. Hofmann, S. Pollmann / Plant Physiology and Biochemistry 46 (2008) 302e308 307
Fig. 7. Superposition of AOC1 (1ZVC) and AOC2 (2BRJ). Both proteins are
shown in ribbon representation (AOC2 in gray, AOC1 in blue). The sidechains
of residues of AOC2 which are mutated in AOC1 are shown as stick models
and labeled. Figure produced with Pymol [5].
expect any large structural differences to AOC1 or AOC2,
the comparison will improve our understanding of the critical
regions of the enzyme.
Acknowledgements
We thank Dr Florian Schaller and Dr Philipp Zerbe for their
discussions and help with figure preparation. This work was
Fig. 6. Proposed cyclization reaction mechanism. Substrate, product and inter- funded by grants from the Deutsche Forschungsgemeinschaft
mediates are shown as structural formulas, important amino acids are shown as
(DFG), Bonn SCHA939 and HO2600 for EH, SFB480, project
rendered sticks. For details see text.
A-10 for SP.
found to be located close to the active site, which is consistent
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