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PROTEIN CHEMISTRY
 
 

• Manel Camps (METX) Use of Random Mutagenesis for Studies of Evolution and for Therapy
• Phil Crews (Chem) Marine Natural Products as Potent Agents Against Human Disease
• Ted Holman (Chem) Lipoxygenase Inhibitors as Potential Anti-Inflammatory Drugs
• Kevin Karplus (BME) Protein Structure Prediction and Design
• Dave Kliger (Chem) Visual Pigment and Heme Proteins, Light, and Biological Processes
• Doug Kellogg (MCD) Control of Cell Growth and Size
• Glenn Millhauser (Chem) Remarkable Protein Structures... and Where They Go Wrong in Disease
• Carrie Partch (Chem) Exploring the Molecular Basis for Circadian Timekeeping in Mammals
• Jevgenij Raskatov (Chem) Disease-Oriented Chemical Biology
• Seth Rubin (Chem) Molecular Mechanisms of Cell Cycle Regulation and Cancer
• Michael Stone (Chem) Structure, Function, and Assembly of the Telomerase Ribonucleoprotein
• Karen Ottemann (METX) How Bacterial Pathogens Sense and Respond to Host Environments
• Fitnat Yildiz (METX) Ex-vivo Survival Mechanisms Used by Vibrio cholerae

Prof Manel CampsUse of Random Mutagenesis for Studies of Evolution and for Therapy

Manel Camps, Microbiology and Environmental Toxicology

The Camps laboratory uses molecular genetic and computational approaches to study the biological consequences of random changes in genetic information (mutations) that occur spontaneously or as a result of environmental insults. Camps' group couples the generation of random mutant libraries with specific selections or screens to study the functional impact of point mutations and to establish how genes evolve to create new biological activities under selective pressure. This work is relevant for the identification of risk factors of disease, understanding the origins of drug resistance, and engineering enzymatic activities. The Camps laboratory also use induction of random genetic alterations (mutagenesis) as an indicator of DNA damage for high-throughput screening of chemical libraries to identify DNA damaging agents. Through this approach, the Camps aims at exploiting the particular susceptibility of rapidly replicating cells to DNA damage for therapeutic purposes in and effort to find lead compounds that complement or enhance existing anti-tumor therapies. [More]
Camps' Publications Manel Camps' Email

Prof Phil CrewsMarine Natural Products as Potent Agents Against Human Disease

Phil Crews, Dept. of Chemistry and Biochemistry

A primary goal of Phillip Crews' marine natural products research is to understand the chemistry of tropical marine sponges. Using bioassay-guided isolation assists us in the discovery of natural products potent against human diseases, such as cancer or viruses. Their search for novel active compounds incorporates elements of structure elucidation, but there are other dimensions to this research, including questions in the areas of chemical ecology, marine natural products biosynthesis, and the relationship between secondary metabolite chemistry and taxonomy... [More]

Crews' Publications Phil Crews' E-Mail

Prof HolmanLipoxygenase Inhibitors as Potential Anti-Inflammatory Drugs

Ted Holman, Dept. of Chemistry & Biochemistry

Lipoxygenases are enzymes implicated in a broad range of inflammatory diseases, such as diabetes, heart disease, and stroke, to name a few. Ted Holman's laboratory examines the enzymatic mechanism and biological function of lipoxygenase in the hopes of understanding how the enzyme functions and developing novel inhibitors. In collaboration with medical school collaborators, his laboratory has identified potent lipoxygenase inhibitors and are currently characterizing their structure/function reactivity. The results of this work will shed light on their potential as anti-inflammatory agents. [More]

Holman's Publications Ted Holman's E-Mail

Prof Kevin KarplusProtein Structure Prediction and Design

Kevin Karplus, Dept. of Biomolecular Engineering

Kevin Karplus' research group develops tools and techniques for protein structure prediction and protein design. He collaborates with Richard Hughey's group on the development of the SAM tool suite for profile hidden Markov models, particularly on developing protocols for using the tools for high-accuracy detection of remote relationships between proteins. Karplus' group has used these tools themselves to earn an international reputation for accurate prediction of protein structure: secondary structure, tertiary structure, and contact prediction. In the biannual Critical Assessment of Structure Prediction "contests", his group has presented papers (the "prize" for the contest) in CASP2 through CASP7. The group also collaborates extensively with UCSC wet-lab biologists in predicting structure and function for proteins of interest to them, and is starting work on designing novel proteins. [More]

Karplus Publications Kevin Karplus's E-Mail

Prof Kliger

Dynamics of Biomedical Molecules in Vision, Allostery, and Folding

David Kliger, Chemistry & Biochemistry

The Kliger lab uses time-resolved spectroscopy to study protein reactions. Proteins are central to health, making study of their structure and function critical. While traditional biochemical methods provide insight about the later steps in function, modern optical methods (particularly pulsed lasers and polarized light) reveal previously unknown steps occurring on short time scales, which are important in biomedical processes. Such information can lead to new insights into fundamental biological processes, as well as guides to the development of new and more effective drug therapies. [More]

Kliger Publications Dave Kliger's Email

Prof KelloggControl of Cell Growth and Size

Doug Kellogg, Dept. of MCD Biology

Cells show extraordinary diversity in size and shape.  The mechanisms by which cells control their growth and size are poorly understood and represent a fundamental unsolved problem in cell biology.  The goal of the Kellogg laboratory's work is to elucidate these mechanisms. Their approach is to use biochemistry, genetics, and mathematical modeling to understand signaling networks that are required for control of cell size and cell growth. [More]
Kellogg's Publications Doug Kellogg's E-Mail

Prof MillhauserRemarkable Protein Structures... and Where They Go Wrong in Disease

Glenn Millhauser, Dept. of Chemistry and Biochemistry

In modern biochemistry, structural determination is essential for understanding the function of biomolecules. Scientists in Glenn Millhauser's laboratory use peptide synthesis, nuclear magnetic resonance spectroscopy (NMR), and electron paramagnetic spin resonance spectroscopy (EPR) to examine the structure and analyze the function of proteins that have been implicated in several debilitating diseases. This includes the prion protein, which is responsible for mad cow disease and the related human affliction, Creutzfeldt-Jakob disease. They have also examined a novel signaling molecule, called AGRP, which is involved in energy balance and metabolic pathologies, such as diabetes and obesity. [More]
Millhauser Publications Glenn Millhauser's E-Mail

Prof Rubin Exploring the Molecular Basis for Circadian Timekeeping in Mammals

Carrie Partch , Chemistry and Biochemistry

Mammalian physiology is synchronized into 24-hour rhythms that coincide with the solar day by an intrinsic molecular clock. As a global regulator of homeostasis, disruption of the circadian clock has profound consequences on human health, leading to depression, metabolic syndromes, cancer, and premature aging. The Partch lab studies how the 24-hour periodicity of this molecular clock is generated and how it integrates with the cell cycle to limit proliferation using cell biology, biochemistry and biophysical techniques. They are also interested in chemical biology approaches to modulate clock timing with structurally informed in vitro and cell-based screening platforms. [More]

Partch Publications Carrie Partch's E-Mail


Prof Karen OttemannHow Bacterial Pathogens Sense and Respond to Host Environments

Karen Ottemann, Dept. of Microbiology and Environmental Toxicology

Professor Karen Ottemann's laboratory investigates how bacteria translate chemical and physical cues in their host environment into pathogenic outcomes. Mistakes in sensation and subsequent gene expression by bacteria may result in their elimination by the host immune response or peristaltic flow. Elucidation of such processes will hopefully lead to identification of anti-bacterial drug targets. Ottemann is particularly interested in the role of outer membrane proteins and chemotaxis associated with the bacterium Helicobacter pylori. This pathogen infects some 3 billion humans and can lead to serious disease, including ulcers and cancer. [More]

Ottemann Publications Karen Ottemann's Email

Prof. Jevgenij A. RaskatovDisease-Oriented Chemical Biology

Jevgenij A. Raskatov, Dept. of Chemistry and Biochemistry

Raskatov draws inspiration from aging-related medicinally challenging questions, which are becoming increasingly pressing as life expectancy continues to rise (the cancer/inflammation interface is of specific interest). Raskatov's lab identifies biomolecular signaling nodes that are sufficiently well-understood at the molecular level, so that a biology problem can be translated into a chemistry problem. As chemists, their goal is to synthesize molecules and study their properties by means of NMR spectroscopy (1), crystallography (2) and DFT computation (3). Molecular scaffolds that show initial promise are tested in relevant biological systems both in cell culture (4) and in vivo (5). [More]

Raskatov Publications Jevgenij Raskatov's Email

Prof RubinMolecular Mechanisms of Cell Cycle Regulation and Cancer

Seth Rubin, Chemistry and Biochemistry

The Rubin laboratory uses a variety of structural and biochemical techniques to investigate the molecular mechanisms that control the eukaryotic cell cycle. The aim is to elucidate detailed molecular pictures of protein-protein interactions and how these interactions are regulated by structural and chemical modifications. Improper regulation of these protein interaction networks is commonly associated with aberrant cell proliferation and cancer. [More]

Rubin Publications Seth Rubin's E-Mail


Prof Michael StoneAssembly, Structure, and Regulation of the Telomerase Ribonucleoprotein

Michael Stone, Dept. of Chemistry and Biochemistry

The Stone Research Group combines the use of biochemical and structural methods with newly emerging single-molecule techniques to probe the dynamics of protein-nucleic acid interactions and the molecular mechanisms of biological motors.  Our current area of focus is the structure and function of the telomerase ribonucleoprotein, an RNA-dependent DNA polymerase that maintains genomic stability by synthesizing repetitive DNA sequences at chromosome termini.  These short DNA repeats provide the foundation for specialized chromatin structures, called telomeres, which prevent deleterious chromosome fusion events by differentiating chromosome ends from sites of DNA damage.  It has been shown that telomere length typically decreases with every round of cell division, leading to the so-called ‘molecular clock’ hypothesis, wherein telomere length serves as a signal to control cellular lifespan. This notion is consistent with the finding that active telomere DNA synthesis is normally restricted to rapidly dividing cell types such as stem cells and the majority of human cancers. Our research seeks to elucidate physical mechanisms governing telomere length regulation, and in turn establish a conceptual framework within which to develop novel diagnostic and therapeutic strategies for human disease. [More]

Stone Publications Michael Stone's Email

Prof Fitnat YildizEx-vivo Survival Mechanisms Used by Vibrio cholerae between Epidemics

Fitnat Yildiz, Dept. of Microbiology and Environmental Toxicology

Ex-vivo Survival Mechanisms used by Vibrio cholerae between Epidemics: Fitnat Yildiz's laboratory investigates signaling and regulatory networks of Vibrio cholerae, the causative agent of the Asiatic cholera. She and her colleagues are particularly interested in those mechanisms that allow the pathogen to adapt to changes in its habitat. The bacteria's ability to survive in different growth modes in aquatic environments is closely linked to seasonal epidemics of cholera. Yildiz's laboratory is attempting to identify and characterize genes and processes associated with phase variations of the pathogen. Their results will be useful for prediction and control of epidemics of this devastating disease. [More]

Yildiz Publications Fitnat Yildiz's E-Mail

 

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