Endowed Chair in Biochemistry and Molecular Biotechnology I
School of Public Health and Health Sciences
Dept of Biochem & Mol Biol And Dept of Chem
Health Informatics And Implementation Science
Rotation Projects Rotation projects are available to address the following questions: How does the lack of structure in the C-terminal zinc finger of TTP affect the activity of the protein in the cell? In humans, there are three members in the TTP protein family: TTP, TIS11b and TIS11d. Structural studies performed by us and others have shown that while the TZF domain of TTP is partially unstructured in the free state and folds upon binding RNA, those of TIS11d and TIS11b are always folded. We have shown that the degree of structure of the TZF domain affects the activity of the protein in cells and indicates that the protein can modulate its activity through its dynamics. We want to determine whether structural disorder is directly linked to cellular stability or protein localization How do mutations in the RNA-binding domain of TIS11d cause cancer? Several point mutation in TTP and TIS11d have been linked to cancer. In particular, point mutations in the RNA-binding domain of TIS11d are found in leukemia patients. We are currently working on the characterization of the structure, dynamics and biological activity of these mutant proteins to understand their role in the pathogenesis of cancer. How does HuR regulate the stability of its target mRNA? HuR is another protein that, like TTP, binds to AU-rich elements (ARE) in mRNAs and regulate their stability. The detailed mechanisms that determine how HuR regulates transcripts stability are poorly understood. We are investigating how binding or HuR to the 3’UTR of an mRNA leads to its stabilization.
The project aims to develop computational algorithms and software programs for analyzing high-throughput sequence data such as ChIP-Seq RNA-Seq small RNA sequencing data. PhD required. A strong background in computational biology especially experience with analyzing high-throughput sequencing data is highly desirable. Excellent communication and writing skills and the ability to work with experimental and computational collaborators are essential. To apply please forward CV cover letter and three references to: Zhiping.Weng@umassmed.edu
Please contact Dr. Weng for information on rotations that are available in her lab.
Paul J. DiMare Chair in Neurodegenerative Disease
Rotation Projects: See our lab webpage for more information on Research Projects: https://www.umassmed.edu/boscolab
Elucidating the factors involved in sporadic ALS and investigating protein misfunction associated with neurodegenerative disease.
Donna M. and Robert J. Manning Chair in Neurosciences
Dr. Brown’s laboratory has focused on the identification of gene defects that elucidate the molecular pathogenesis of selected neuromuscular diseases including amyotrophic lateral sclerosis (ALS, also known as Lou Gehrig’s disease), muscular dystrophy, adrenoleukodystrophy, hereditary neuropathy and hyperkalemic periodic paralysis.
Dr. Esteves is a neuroscientist with interest in gene therapy to help treat neurodegenerative diseases.
Rotation projects We apply X-ray crystallography and biochemical methods to understand the mechanisms employed by the ribosome. Potential rotation projects are 1) to understand various aspects of translation via mutagenesis/biochemical assays, 2) to crystallize and work on determining the structures of translation factors and functional ribosome complexes, and 3) to improve computational methods used to determine crystal structures of macromolecules. Feel free to contact the lab for a more detailed discussion.
Potential Rotation Projects Mapping glucose transporter ligand binding sites. Mapping GLUT1 intramolecular contacts. How does cell shape regulate glucose transport? Using transporter chimeras to map specificity and functional domains. Development of a transwell model for blood brain barrier function. Site directed GLUT1 mutagenesis to test specific hypotheses for GLUT1 function. For specific details on each project, please e-mail me at: anthony.carruthers@umassmed.edu
Project 1 Investigate the lethal expression of P35 in dam lysogens. Plus inducer No inducer Lysogenic cultures of p35/dam (top) and p35/wildtype (bottom) were diluted and aliquots spotted on media with and without inducer.
Neil and Margery Blacklow Chair in Infectious Diseases and Immunology
<Long Text /> Potential Rotation Projects Project #1: Probing the structural basis for cooperativity in a dimeric hemoglobin: Scapharca dimeric hemoglobin is an elegantly simple model system for exploring the structural basis for intersubunit communication. Our analysis to date has established a new paradigm for cooperativity in which tightly bound water molecules are used as sensors for ligand state. In this project, the student will first mutate the gene for the native hemoglobin at a residue that is suspected of playing a role in the intersubunit communication. The mutated protein will then be expressed in E. coli and purified and subjected to functional analysis of oxygen binding. Using conditions already established for the native protein, the mutant hemoglobin will then be crystallized and subjected to preliminary x-ray analysis. This project will provide the student with an introduction to two of the most powerful techniques for investigating the structure and function of proteins: site-directed mutagenesis and x-ray crystallography. Additionally, valuable experience in protein purification will be obtained. Project #2: Structural analysis of the polymerization of sickle-cell hemoglobin Sickle cell disease results from the pathological polymerization of deoxygenated hemoglobin S (ß6E->V) within erythrocytes. This polymerization depends upon a complicated interplay of multiple interactions between tetramers. Our high resolution crystal structure of this molecule has elucidated details of some of the important interactions. Several projects are available for rotation students. These include crystallization of sickle-cell hemoglobin in the presence of an inhibitor to identify its binding site, site-directed mutagenesis of hemoglobin S and crystallization of mutants that show altered polymerization characteristics.
Gretchen Stone Cook Chair in Biomedical Sciences
A postdoctoral position is available to study in this laboratory. Contact Dr. Zamore for additional details
Potential Rotation Projects Our laboratory uses a combination of biochemistry, cell biology, and genetics to dissect the RNAi pathway. A rotation project is available to explore the mechanisms that underlie the RNAi phenomenon or the biological pathways in which RNAi enzymes participate in flies, mice and humans.
Arthur F. and Helen P. Koskinas Professor in Biochemistry and Molecular Biotechnology
Motor Neuron Disease Mechanisms; Hyperkalemic Periodic Paralysis: a Muscle Ion Channel Disorder.
Potential Rotation Projects One of the five most common structural classes of proteins is the (b/a)8 barrel motif. These proteins have eight parallel b strands arranged in a cylindrical fashion in the hydrophobic core and a corresponding number of amphipathic a-helices that dock on the surface of this cylinder. Equilibrium and kinetic studies of the folding reaction of one representative of this class, the subunit of tryptophan synthase, have shown that this single, symmetrical domain is formed by the progressive development of structure and stability in two partially folded forms. We are currently exploring the folding mechanisms of other (b/a)8 barrel proteins. Our goal for comparing the folding mechanisms of different members of the (b/a)8 barrel family is to learn how sequence relates to folding mechanism. The laboratory rotation would involve studying the equilibrium folding properties of another member of this structural class. Experiences that would be gained include expertise in protein expression and purification, and the collection and analysis of data acquired by spectroscopic techniques such as circular dichroism and fluorescence. Understanding the mechanism of folding and assembly of oligomeric peptides and proteins will provide important insights into a process that is essential for all forms of life. One model system that we have been using to study multimeric folding events is the homodimeric leucine zipper peptide, GCN4-p1. Mutational studies have yielded insights into the roles of helix propensity, salt bridges and buried polar residues in the transition state for folding. We are currently extending these studies to explore the folding and assembly of heterodimeric and heterotrimeric coiled coils. This rotation will provide training in peptide synthesis, HPLC purification, ultracentrifugation, circular dichroism spectroscopy, fluorescence resonance energy transfer experiments, and data analysis. The mechanism by which natural proteins fold to their functional forms has been evolutionarily selected to be relevant on a biological time scale. Synthetic proteins, while designed to achieve stable native forms, have not had evolutionary pressures applied to remove kinetic traps in their folding mechanisms and may have complicated access routes to their native states. By studying the folding of five synthetic ßa-repeat proteins, we will test the proposition that the design principles not only achieve the native state but do so via relatively smooth energy landscapes (Baker lab, Nature 2013). The project will involve the expression and purification of the synthetic proteins and their biophysical characterization, with a focus on the early folding events<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p>
A postdoctoral position is available to study in this laboratory. Contact Dr. Lambright for additional details.
Lab Rotations <p >Our lab takes an interdisciplinary approach to the study of fundamental problems in cell biology, signal transduction and membrane trafficking. Rotation projects are available in any of the areas of interest to the lab. Projects are tailored to the individual interests of the students and often involve a combination of molecular, biochemical, biophysical, structural and/or cell based analyses to investigate signaling and trafficking mechanisms. <p >
One postdoctoral position is available to study the mechanism and treatment of motor neuron disease. Experience in molecular biology and neuroscience is preferred. Contact Dr. Xu for additional details.
Rotation Project Background
In yeast cells, protein translocation across the endoplasmic reticulum can occur by cotranslational or posttranslational pathways. The objective of this project is to develop a rapid method to inactivate the posttranslational pathway in vivo in yeast cells by appending the CMV-ribosome stalling sequence to the C-terminus of a typical posttranslational translocation substrate (carboxypeptidase Y). Complexes between the posttranslational translocation channel (SEC complex) and the stalled ribosomes will be purified for structural and functional analysis.
A postdoctoral position is available to study in this laboratory. Contact Dr. Craig for additional details.
Potential Rotation Projects Project #1: Lipid-Layer Protein Crystallization for Electron Microscopy.While individual protein molecules can be readily visualized by EM, structural information is greatly enhanced if the molecules can by crystallized into 2-dimensional ordered arrays. Methods for achieving this are well established, making use of lipid monolayers at an air-water interface. Follow literature methods to crystallize "standard" proteins using the lipid-layer method. Observe results by electron microscopy following negative staining. If time permits, carry out preliminary image processing of micrographs and/or crystallization of unknown proteins. Techniques to be learned: lipid layer crystallization methods; grid preparation; use of electron microscope; image processing.
Potential Rotation Projects Several rotation projects are available in structural biology of immune receptors, antigen presentation pathways, T-cell activation, and development of novel T-cell detection reagents. Please see Prof. Stern for details.
Maroun Semaan Chair in Biomedical Research
A postdoctoral position is available to study in this laboratory. Please contact Dr. Walhout for additional details.
Rotation Projects <p >We have identified a number of bacterial pathways that are required for bacterial viability or virulence. We are particularly interested in: Phosphosignaling systems that regulate cell wall synthesis Metabolic regulatory mechanisms that trigger the “dormancy” response observed during infection. <p >A variety of genetic, biochemical, and informatic methods will be used to define the functions of these genes and the role played by each during infection. <p >
<p >Rotation Projects <p >Rotation projects are designed to expose students to the molecular cell biology of solid tumors and to provide them with an appreciation for translational cancer research. Specific rotation projects, which are focused on the major themes of the lab, include: <p >Function and Regulation of Integrins (Cell Adhesion Receptors) in Cancer Epigenetic mechanisms that regulate integrin gene expression in human cancers Regulation of integrin expression and function during the EMT Role of specfic microRNAs (miRs) in regulating integrin function and signaling Contribution of integrins to carcinoma progression using mouse models of breast carcinoma <p >Vascular Endothelial Growth Factor (VEGF) Signaling, EMT and Carcinoma Progression Function and expression of VEGF receptors in carcinoma cells Regulation of VEGF transcription in response to EMT stimuli Role of miRs in regulating VEGF receptors and signaling Contribution of VEGF signaling to the behavior of aggressive, de-differentiated carcinomas <p >Nuclear Hormone Receptors and EMT Role of estrogen receptors in regulating the EMT Regulation of VEGF transcription by estrogen receptors
Potential Rotation Projects <p >Our laboratory combines genetic and biochemical approaches to investigate the molecular underpinnings of adaptation. Potential rotation projects are available in two general (and partially overlapping) areas: exploring fitness landscapes through systematic approaches and investigating the molecular mechanism of the Hsp90 chaperone in signal transduction. Please contact the lab to discuss specific rotation projects in more detail.
Teresita del Nino Jesus Padilla-Benavides PhD
Claudia A. Vilchis Nestor. Visiting Scholar from CINVESTAV-IPN, MEXICO
Population and Quantitative Health Sciences
Focus: The Munro laboratory develops and applies quantitative biophysical approaches to visualize virus replication, and probe the functions of the proteins and RNAs involved.
Biochemistry and Molecular Biotechnology