Owen M. McDougal

Recycling of Waste Acetone by Fractional Distillation

Nicholas A. Weires et al. — Wed, 04 Jan 2012 13:50:31 PST

Distillation is a ubiquitous technique in the undergraduate organic chemistry curriculum; the technique dates back to ca. 3500 B.C.E. With the emergence of green chemistry in the 1990s, the importance of emphasizing responsible waste management practices for future scientists is paramount. Combining the practice of distillation with the message that waste generation should be minimized conveys green concepts from the beginning of the student’s experience in the lab. In this experiment, acetone waste collected from the cleaning of student glassware is purified by fractional distillation. The purity of the resulting distillate is determined by refractive index and density calculation. The distilled acetone is of sufficient purity (88%) that students can reuse it to wash glassware, collect the waste, and add it to a communal still that is operated by the instructor or support personnel. Students learn how to set up and perform a fractional distillation experiment, learn how to test the distillate for purity by refractive index and density, and are exposed to the value of recycling materials for reuse. The communal distillation apparatus provides an ongoing source of purified acetone for students to use throughout the remainder of the term.

Proteomic Analysis of Col11a1-associated Protein Complexes

Raquel Brown et al. — Wed, 04 Jan 2012 13:50:30 PST

Cartilage plays an essential role during skeletal development within the growth plate and in articular joint function. Interactions between the collagen fibrils and other extracellular matrix molecules maintain structural integrity of cartilage, orchestrate complex dynamic events during embryonic development, and help to regulate fibrillogenesis. To increase our understanding of these events, affinity chromatography and liquid chromatography/tandem mass spectrometry were used to identify proteins that interact with the collagen fibril surface via the amino terminal domain of collagen alpha 1(XI) a protein domain that is displayed at the surface of heterotypic collagen fibrils of cartilage. Proteins extracted from fetal bovine cartilage using homogenization in high ionic strength buffer were selected based on affinity for the amino terminal noncollagenous domain of collagen alpha 1(XI). Mass spectrometry was used to determine the amino acid sequence of tryptic fragments for protein identification. Extracellular matrix molecules and cellular proteins that were identified as interacting with the amino terminal domain of collagen alpha 1(XI) directly or indirectly, included proteoglycans, collagens, and matricellular molecules, some of which also play a role in fibrillogenesis, while others are known to function in the maintenance of tissue integrity. Characterization of these molecular interactions will provide a more thorough understanding of how the extracellular matrix molecules of cartilage interact and what role collagen XI plays in the process of fibrillogenesis and maintenance of tissue integrity. Such information will aid tissue engineering and cartilage regeneration efforts to treat cartilage tissue damage and degeneration

DockoMatic: Automated Peptide Analog Creation for High Throughput Virtual Screening

Reed B. Jacob et al. — Fri, 09 Sep 2011 09:30:40 PDT

The purpose of this manuscript is threefold: (1) to describe an update to DockoMatic that allows the user to generate cyclic peptide analog structure files based on protein database (pdb) files, (2) to test the accuracy of the peptide analog structure generation utility, and (3) to evaluate the high throughput capacity of DockoMatic. The DockoMatic graphical user interface interfaces with the software program Treepack to create user defined peptide analogs. To validate this approach, DockoMatic produced cyclic peptide analogs were tested for three-dimensional structure consistency and binding affinity against four experimentally determined peptide structure files available in the Research Collaboratory for Structural Bioinformatics database. The peptides used to evaluate this new functionality were alpha-conotoxins ImI, PnIA, and their published analogs. Peptide analogs were generated by DockoMatic and tested for their ability to bind to X-ray crystal structure models of the acetylcholine binding protein originating from Aplysia californica. The results, consisting of more than 300 simulations, demonstrate that DockoMatic predicts the binding energy of peptide structures to within 3.5 kcal mol⁻¹, and the orientation of bound ligand compares to within 1.8 Å root mean square deviation for ligand structures as compared to experimental data. Evaluation of high throughput virtual screening capacity demonstrated that Dockomatic can collect, evaluate, and summarize the output of 10,000 AutoDock jobs in less than 2 hours of computational time, while 100,000 jobs requires approximately 15 hours and 1,000,000 jobs is estimated to take up to a week.

A Practical Method for the Display of High Resolution One- and Two-Dimensional NMR Spectra on the World Wide Web

Coyner B. Graf et al. — Tue, 02 Aug 2011 14:13:50 PDT

A system to display interactive high resolution one- and two-dimensional nuclear magnetic resonance (NMR) spectra on the World Wide Web is presented. This practical method may be reproduced, implemented, and applied to the creation of online libraries of NMR spectra at other venues.

Biomass Briquettes: Turning Waste into Energy

Owen McDougal et al. — Thu, 26 May 2011 15:53:35 PDT

Fuel briquettes generated by the low-pressure compaction of paper, sawdust, agricultural or yard waste, etc. currently serve as an alternative to firewood, wood pellets and charcoal in developing countries in Africa, Asia and South America. Research at Boise State University in Idaho, explored both the caloric content and shape to optimize burn efficiency of the biobriquettes. The energy content of briquettes ranged from 4.48 to 5.95 kilojoule per gram (kJ/g) depending on composition, whereas the energy content of sawdust, charcoal and wood pellets ranged from 7.24 to 8.25 kJ/g. Biobriquettes molded into a hollow-core cylindrical form exhibited energy output comparable to that of traditional fuels. The study demonstrates that low-energy content feedstocks can be composted, pressed and combusted to produce heat output commensurate with higher energy content fuels.

DockoMatic - Automated Ligand Creation and Docking

Casey W. Bullock et al. — Fri, 19 Nov 2010 11:54:42 PST

Background: The application of computational modeling to rationally design drugs and characterize macro biomolecular receptors has proven increasingly useful due to the accessibility of computing clusters and clouds. AutoDock is a well-known and powerful software program used to model ligand to receptor binding interactions. In its current version, AutoDock requires significant amounts of user time to setup and run jobs, and collect results. This paper presents DockoMatic, a user friendly Graphical User Interface (GUI) application that eases and automates the creation and management of AutoDock jobs for high throughput screening of ligand to receptor interactions. Results: DockoMatic allows the user to invoke and manage AutoDock jobs on a single computer or cluster, including jobs for evaluating secondary ligand interactions. It also automates the process of collecting, summarizing, and viewing results. In addition, DockoMatic automates creation of peptide ligand .pdb files from strings of single-letter amino acid abbreviations. Conclusions: DockoMatic significantly reduces the complexity of managing multiple AutoDock jobs by facilitating ligand and AutoDock job creation and management.

Three-Dimensional Structure of Conotoxin tx3a: A m-1 Branch Peptide of the M-Superfamily

Owen M. McDougal et al. — Wed, 17 Nov 2010 08:00:55 PST

The M-superfamily, one of eight major conotoxin superfamilies found in the venom of the cone snail, contains a Cys framework with disulfide-linked loops labeled 1, 2, and 3 (- CC¹C²C³CC-). M-superfamily conotoxins can be divided into the m-1, -2, -3 and -4 branches, based upon the number of residues located in the third Cys loop between the fourth and fifth Cys residues. Here we provide a three-dimensional solution structure for the m-1 conotoxin tx3a found in the venom of Conus textile. The 15 amino acid peptide, CCSWDVCDHPSCTCC, has disulfide bonds between Cys¹ and Cys¹⁴, Cys² and Cys¹², and Cys⁷ and Cys¹⁵ typical of the C1- C5, C2-C4, and C3-C6 connectivity pattern seen in m-1 branch peptides. The tertiary structure of tx3a was determined by 2D ¹H NMR in combination with the combined assignment and dynamics algorithm for nuclear magnetic resonance (NMR) applications CYANA program. Input for structure calculations consisted of 62 inter- and intraproton, 5 phi angle, and 4 hydrogen bond constraints. The root-mean-square deviation values for the 20 final structures are 0.32 +/- 0.07 Å and 0.84 +/- 0.11 Å for the backbone and heavy atoms, respectively. Surprisingly, the structure of tx3a has a “triple-turn” motif seen in the m-2 branch conotoxin mr3a, which is absent in mr3e, the only other member of the m-1 branch of the M-superfamily whose structure is known. Interestingly, injection of tx3a into mice elicits an excitatory response similar to that of the m-2 branch peptide mr3a, even though the conotoxins have different disulfide connectivity patterns.

The M-Superfamily of Conotoxins: A Review

Reed B. Jacob et al. — Thu, 04 Nov 2010 13:14:26 PDT

Throughout the world there exist both predator and prey. This distinction is apparent though sometimes misleading. Take for example marine snails of the genus Conus that are present across the oceans of the southern hemisphere [1]. These snails are slow moving animals that appear more prey than predator. However, they have evolved into effective predators through the development of venom consisting of biologically active peptides. The venom is loaded into a hollow harpoon that the snail injects into the intended prey: fish, worms, or other snails [2]. The categories of cone snails based on prey preference are piscivorous (fish eating), molluscivorous (mollusk eating), and vermivorous (worm eating) [3]. The cone snail venom contains myriad peptide components significant to the survival of the organism with respect to hunting and defense against being eaten [4]. Interest by researchers in snails of the genus Conus began in the early nineteen seventies as evidence of their involvement in numerous human fatalities mounted [5]. Dr. Alan Kohn, an early pioneer in the study of hunter/prey relationship of cone snails, recognized that the venom of cone snails may possess therapeutic components [6]. During that time, Dr. Robert Endean and coworkers in Australia demonstrated that the venom of dissimilar species of cone snail contained a diversity of biologically active components. Dr. Baldomero (Toto) Olivera and coworkers at the University of Utah became the primary innovators of successful laboratory techniques in the study of venom components extracted from cone snails [7]. Foremost among these innovations was an avant-garde method of bio-assay using intracranial rather than intraperitoneal injection of toxin into subject mice. This new delivery method revealed greater sensitivity to individual peptides in fish and mouse studies than those from standard M-superfamily intraperitoneal injections [8]. This early research revealed the disulfide rich nature of the majority of peptide components from Conus snail venom. The disulfide rich peptides became broadly defined as conotoxins [9].

Finding MRSA’s Kryptonite: Computational Directed Combatant Pentapeptides

Reed B. Jacob et al. — Fri, 29 Oct 2010 13:11:41 PDT

Introduction to Organic and Biological Chemistry

Owen M. McDougal et al. — Fri, 29 Oct 2010 12:55:27 PDT

Introduction to Organic and Biological Chemistry

Owen M. McDougal et al. — Fri, 29 Oct 2010 12:52:44 PDT

Structural Basis for α-Conotoxin Potency and Selectivity

Matt Turner et al. — Tue, 22 Sep 2009 15:50:25 PDT

Parkinson’s disease is a debilitating movement disorder characterized by altered levels of α₆β₂* nicotinic acetylcholine receptors (nAChRs) localized on presynaptic striatal catecholaminergic neurons. α-Conotoxin MII (α-CTx MII) is a highly useful ligand to probe α₆ß₂ nAChRs structure and function, but it does not discriminate among closely related α₆* nAChR subtypes. Modification of the α-CTx MII primary sequence led to the identification of α-CTx MII[E11A], an analog with 500-5300 fold discrimination between α₆* subtypes found in both human and non-human primates. α-CTx MII[E11A] binds most strongly (femtomolar dissociation constant) to the high affinity α₆* nAChR, a subtype that is selectively lost in Parkinson's disease. Here we present the three-dimensional solution structure for α-CTx MII[E11A] as determined by two-dimensional 1H NMR spectroscopy to 0.13 +/- 0.09 Ǻ backbone and 0.45 +/- 0.08 Ǻ heavy atom root mean square deviation from mean structure. Structural comparisons suggest that the increased hydrophobic area of α-CTx MII[E11A] relative to other members of the α-CTx family may be responsible for its exceptionally high affinity for α₆α₄β₂* nAChR as well as discrimination between α₆ß₂ and α₃β₂ containing nAChRs. This finding may enable the rational design of novel peptide analogs that demonstrate enhanced specificity for α₆* nAChR subunit interfaces and provide a means to better understand nAChR structural determinants that modulate brain dopamine levels and the pathophysiology of Parkinson's disease.