One of the most heavily researched proteins in existence, cytochrome c has proved irresistible to chemists and biophysicists for decades. This volume serves as a source book to update the vast body of literature compiled on this protein over the last 40 years. Chapters from an internationally renowned group of experts provide extensive coverage of structural studies, spectroscopic properties, thermodynamic properties, electron transfer kinetics and protein modification. "... a valuable addition to the cytochrome literature; I will certainly get a copy for my group." Dr G. R. Moore, University of East Anglia "For any and all students of the science of cytochrome c, this is an indispensable text." SIM News

Chemistry and chemical engineering have changed significantly in the last decade. They have broadened their scopeâ€"into biology, nanotechnology, materials science, computation, and advanced methods of process systems engineering and controlâ€"so much that the programs in most chemistry and chemical engineering departments now barely resemble the classical notion of chemistry. Beyond the Molecular Frontier brings together research, discovery, and invention across the entire spectrum of the chemical sciencesâ€"from fundamental, molecular-level chemistry to large-scale chemical processing technology. This reflects the way the field has evolved, the synergy at universities between research and education in chemistry and chemical engineering, and the way chemists and chemical engineers work together in industry. The astonishing developments in science and engineering during the 20th century have made it possible to dream of new goals that might previously have been considered unthinkable. This book identifies the key opportunities and challenges for the chemical sciences, from basic research to societal needs and from terrorism defense to environmental protection, and it looks at the ways in which chemists and chemical engineers can work together to contribute to an improved future.

Directed evolution of E. coli for improved small-molecule production requires a combination of rational design and high-throughput screening technologies. Rational design-based directed evolution schemes use structural analyses and metabolic models to help identify targets for mutagenesis, thus improving the likelihood of identifying the desired phenotype. We used a strictly rational design-based approach to re-engineer cytochrome P450BM3 for epoxidation of amorphadiene, developing a novel route for production of the anti-malarial compound artemisinin. A model structure of the lowest energy transition state complex for amorphadiene in the P450BM3 active site was created using ROSETTA-based energy minimization. The resulting enzyme variant produced artemisinic-11S,12-epoxide at titers greater than 250 mg*l-1. Continued attempts to use ROSETTA and to either improve P450BM3 epoxidase activity or introduce hydroxylase activity, however, proved unsuccessful. In the absence of a high-throughput screening approach, further improvement of the P450-based production system would be difficult. As with most small-molecules, there exists no known high-throughput screen for artemisinic-11S-12-epoxide, amorphadiene, or any structurally-related compound. We hypothesized that a generalized method for high-throughput screen or selection design could be based on transcription factor-promoter pairs responding to the target small-molecule. Transcription factors have long been used to construct whole-cell biosensors for the detection of environmental small-molecule pollutants1, but the work has remained largely un-translated toward screen development. While no known transcription factor binds artemisinic epoxide, a putative transcription factor-promoter pair responsive to 1-butanol, a biofuel molecule of interest in our laboratory, was recently reported2. The transcription factor, BmoR, and its cognate promoter, PBMO, were used to build a short-chain alcohol biosensor for use as a genetic screen or selection. Following optimization of expression temperature, promoter, and reporter 5'-untranslated region, among other parameters, the BmoR-PBMO system was shown to provide robust detection of 1-butanol in an E. coli host. The biosensor transfer function - relating input alcohol concentration to output fluorescent signal - was derived for 1-butanol and structurally related alcohols using the Hill Equation. The biosensor exhibited a linear response between 100 μM and 40 mM 1-butanol, and a dynamic range of over 8000 GFP/OD600 units. A 700 μM difference in 1-butanol concentration could be detected at 95% confidence. By replacing the GFP reporter with TetA, a tetracycline transporter, a 1-butanol selection was constructed; E. coli harboring the TetA-based biosensor exhibited 1-butanol dependent growth in the presence of tetracycline up to 40 mM exogenously added 1-butanol. Demonstration of the biosensor in various high-throughput screening and selection applications first required construction of a 1-butanol production host. Studies have reporter 1-butanol production in E. coli through heterologous expression of either the C. acetobutylicum 1-butanol biosynthetic pathway3, or a 2-keto acid-based pathway composed of a L. lactis 2-keto acid decarboxylase, KivD, and the S. cerevisiae alcohol reductase, ADH64. In our hands, the C. acetobutylicum pathway proved non-robust and yielded low titers. In contrast, high-titer production of user-defined 2-keto acid derived alcohols was achieved by introduction of a [Delta]ilvDAYC knockout in E. coli and expression of KivD and ADH6. The engineered strain is auxotrophic for 2-keto acids, and 1-butanol was produced by supplementing the growth medium with 2-oxopentanoate. A liquid culture screen was demonstrated using a 960-member KivD and ADH6 ribosome binding site library. Using the TetA-based biosensor, a strict cut-off between analyte 1-butanol concentration and biosensor output was observed. The assay led to the identification of a variant 2-keto acid-based alcohol production pathway exhibiting an approximately 20% increase in specific 1-butanol productivity. Attempts to engineer concomitant 1-butanol production and selection in E. coli proved difficult. Both production and detection pathways functioned robustly when individually expressed in engineered E. coli; however, concomitant production and detection resulted in increased plasmid instability and cell death. We conclude by providing an analysis of observed cell stresses, generating negative 1-butanol selective pressures, and outline future strategies that can be used to address these hurdles.

Many potential applications of synthetic and systems biology are relevant to the challenges associated with the detection, surveillance, and responses to emerging and re-emerging infectious diseases. On March 14 and 15, 2011, the Institute of Medicine's (IOM's) Forum on Microbial Threats convened a public workshop in Washington, DC, to explore the current state of the science of synthetic biology, including its dependency on systems biology; discussed the different approaches that scientists are taking to engineer, or reengineer, biological systems; and discussed how the tools and approaches of synthetic and systems biology were being applied to mitigate the risks associated with emerging infectious diseases. The Science and Applications of Synthetic and Systems Biology is organized into sections as a topic-by-topic distillation of the presentations and discussions that took place at the workshop. Its purpose is to present information from relevant experience, to delineate a range of pivotal issues and their respective challenges, and to offer differing perspectives on the topic as discussed and described by the workshop participants. This report also includes a collection of individually authored papers and commentary.

Biological processes in any living organism are based on selective interactions be tween particular biomolecules. In most cases, these interactions involve and are driven by proteins, which are the main conductors of any life process within the organism. The physical nature of these interactions is still not well known. This book presents an entirely new approach to analysis of biomolecular in teractions, in particular protein-protein and protein-DNA interactions, based on the assumption that these interactions are electromagnetic in nature. This new ap proach is the basis of the Resonant Recognition Model (RRM), which was devel oped over the last 15 years. Certain periodicities within the distribution of energies of delocalised electrons along a protein molecule are crucial to the protein's biological function, i.e. inter action with its target. If protein conductivity were introduced, then charges mov ing through the protein backbone might produce electromagnetic irradiation or ab sorption with spectral characteristics corresponding to energy distribution along the protein. The RRM is capable of calculating these spectral characteristics, which we hypothesized would be in the range of the infrared and visible light. These characteristics were confirmed with frequency characteristics obtained ex perimentally for certain light-induced biological processes.

The term 'molecular recognition' refers to the specific interaction between two or more molecules through noncovalent bonding. This book presents research in the study of molecular recognition, including next generation molecular imprinted polymers; applications of molecular imprinting; recent advances in DNA-Ligand molecular recognition and allosteric interactions; the proteomic code and the molecular recognition of odorant-binding proteins in insect olfaction.