Search Google Appliance


Biological Research

Welcome to biological chemistry research at Portland State University. Professors Benight, Iwata-Reuyl, Lehman, Perona, Peyton, Reynolds, Simoyi, and Stuart are active in the field of biochemistry. Our work investigates the chemical basis for biological action with emphases on mechanistic enzymology, drug discovery, and nucleic acid structure-function relationships. The work in these fields is funded by the National Institutes of Health, the National Science Foundation, and the National Aeronautics and Space Administration, to name a few.

Current specializations include studies on the biochemistry of RNA-modifying enzymes, the RNA World and catalytic RNAs, the thermodynamics of DNA-DNA interactions, pathways of bacterial natural product synthesis, and anti-malarial drug strategies. In these endeavors we collaborate frequently with other PSU faculty, researchers at Oregon Health and Sciences University (OHSU), and faculty at many other universities. Facilities on the PSU campus for biological chemistry research include a state-of the-art mass spectrometry center, 400 and 600 MHz NMR spectrometers, and phosphorimaging. Our projects also involve close interactions with the Oregon Translational Research and Development Institute (OTRADI) and private biomedical industry.

Covalent self-assembly of self-replicating RNAs:

Schematic of a self-assembling system of self-replicating RNA molecules.

Schematic of a self-assembling system of self-replicating RNA molecules.

Professor Niles Lehman has developed a system of RNA molecules that can spontaneously covalently self-assemble into a self-replicating ribozyme. The key features of this work have been published in Hayden & Lehman (2006) Chem. Biol. 13, 909-918 and in Hayden et al. (2008) Angew. Chem. Int. Ed. 47, 8424-8428. As many as four independently non-functional RNA oligomers can cooperate to self-assemble a covalent RNA recombinase ribozyme, which can then make more copies of itself in a highly autocatalytic fashion. This system is a model for the origins of self-replication during the RNA World, a proposed period during the origins of life on the Earth some 4 billion years ago. The key process in this covalent self-assembly reaction is recombination, which is the swapping of blocks of genetic information from one molecule to another. As this process is effectively energy neutral, the shuffling of RNA fragments from abiotic oligomers others can, with the application of a selection mechanism, allow for the spontaneous advent of functional RNAs from non-functional ones. This work fits squarely within NASA's mandate to search for life in the universe, and has obvious astrobiological implications.

Development of drugs that are active against drug-resistant diseases:

Illustration of a Mosquito

(Left) - The Mosquito: a malaria vector. (Right) - Reversed chloroquines

Professor David Peyton has developed an approach to drug development that incorporates two drugs into a single ‘hybrid drug' structure. One portion of the hybrid molecule is analogous to the original drug, while the other portion is responsible for countering the drug-resistance mechanism.

The ‘proof of concept' disease for this approach is malaria. The ‘gold standard' of therapy for malaria was chloroquine, but resistance to this inexpensive and otherwise effective drug has spread throughout most of the world. This has resulted in massive numbers of deaths, as well as epic amounts of suffering, and economic devastation. The hybrid molecules, which we termed Reversed Chloroquines (RCQs; Burgess et al. (2006). A chloroquine-like molecule designed to reverse resistance in Plasmodium falciparum. J. Med. Chem. 49, 5623-5625). Research into the action of RCQs has shown this approach to be robust, and a series of drug candidates has been developed with increased potency. A startup company, DesignMedix, Inc., has taken over the task of moving this project toward becoming a drug available to those who need it in the Developing World.

Solution-state structure-function studies of proteins:

Schematic of a self-assembling system of self-replicating RNA molecules.

Collagen

Professor David Peyton is working with other researchers on understanding how protein structures correlate with their physiological functioning, as well as on the mechanisms that impart protein stability. The primary tool for these studies is NMR spectroscopy, and Dr. Peyton is the director of the PSU NMR laboratory. Specific studies are on the collagen triple-helix; collagen being the most abundant mammalian protein, but still with energetics not entirely understood. Other studies include self-chaperoning protein folding mechanisms, as well as viral and microbial infection protein factors.

Mechanistic enzymology and post-transcriptional processing of RNA:

queosine and archaeosine

(Left) - queosine and archaeosine.  (Right) - Biosynthesis of modified nucleosides

The Iwata-Reuyl laboratory is working to elucidate the pathways to a number of structurally complex nucleosides found in RNA, and recently discovered that the first enzyme in the pathway to a class of modified nucleosides that share the 7-deazaguanine structure, such as queuosine and archaeosine, is also the first step in the pathway to the cofactors folic acid and biopterin (Phillips G, El Yacoubi B, Lyons B, Alvarez S, Iwata-Reuyl D, & de Crécy-Lagard V (2008). J. Bacteriol.190, 7876-7884).

The enzyme, GTP cyclohydrolase I (GCYH-I), catalyzes a complex reaction that converts GTP to 7,8-dihydroneopterin triphosphate.

Ribbon diagram of GCYH-IB from Neisseria gonorrhoeae

Ribbon diagram of GCYH-IB from Neisseria gonorrhoeae

Notably, the Iwata-Reuyl lab also discovered a new member of this enzyme class (named GCYH-IB) that is structurally distinct from the canonical enzyme present in other bacteria and humans, and demonstrated that it is present in many pathogenic bacteria (El Yacoubi B, Bonnett S Anderson J, Swairjo MA, Iwata-Reuyl D & de Crécy-Lagard V (2006). J. Biol. Chem. 281, 37586-37593), opening up the possibility of targeting this enzyme with a new generation of antibiotics.

Natural products from microorganisms:

Predicted function of the type I modular polyketide synthase responsible for generating the carbon backbone of phoslactomycins

Predicted function of the type I modular polyketide synthase responsible for generating the carbon backbone of phoslactomycins

The Reynolds lab is investigating microorganisms that produce secondary metabolites or natural products. These compounds find widespread use including antibiotics, immunosuppressants, anticancer agents, and antiparasitic agents. The carbon skeleton cores of many of these compounds are produced by polyketide synthases (PKSs). The Reynolds lab is studying these complex fascinating biosynthetic processes at both the genetic and enzymatic level (e.g., see Sachdeva S, Musayev FN, Alhamadsheh MM, Scarsdale JN, Wright HT, & Reynolds KA (2008). Separate entrance and exit portals for ligand traffic in Mycobacterium tuberculosis FabH. Chem. Biol. 15, 402-412). A combination of genetic techniques, including molecular breeding and in vivo recombination, are being used to generate engineered microorganisms in which the natural biosynthetic process of interest has been diverted, in some cases through the use of catalytically efficient hybrid PKSs.  In combination with chemoenzymatic approaches and precursor-directed mutasynthesis we are producing a wide range of new natural products with a various of biological activities.

Model for the role protein conformational change in binding of the long chain acyl CoA substrate to the mtFabH

Model for the role protein conformational change in binding of the long chain acyl CoA substrate to the mtFabH

Currently the interest is in the phoslactomycin (PLMs) and fostriecin (compounds with antitumor and antifungal activity), hygromycin A and pikromycin (antibacterial activity) and prodiginines (compounds with interesting immunosuppressant, antimalarial and antitumor activites). A library of more than 50 new phoslactomycins has been generated and their biological activities are being evaluated.

A second area of interest in the Reynolds lab is the pathway of plant and bacterial fatty acid biosynthesis, catalyzed by type II fatty acid synthases (FASs). The unique features of this pathway, and of enzyme specific to this process have attracted considerable interest as both targets for both antibiotic development and engineering altered oil composition in bacteria and transgenic plants. 3-Ketoacyl ACP synthase III (KASIII) initiates fatty acid biosynthesis in this process by catalyzing a condensation between an acyl CoA and a malonyl ACP substrate. Different KASIII enzymes from Staphylococci aureus, Escherichia coli, and Mycobacterium tuberculosis (the organism that causes tuberculosis) and Plasmodial falciparum (the parasite responsible for malaria) are being actively investigated. Mutagenesis, molecular modeling, kinetic analyses and X-ray diffraction are being used to probe the mechanism and varying substrate specificities of these enzymes. The M. tuberculosis KASIII has been crystallized and its structure has been solved, and the molecule is now believed to play a critical role in initiating mycolate biosynthesis in this pathogenic microorganism. The lab has designed and synthesized several series of selective synthetic KASIII inhibitors and is using techniques such as molecular modeling and X-ray crystallography with a long-term goal of developing these into a new generation of antimalarial, antibacterial and antituberculosis drugs.