Research
Binding of aspartame and two water molecules to a human sweet taste receptor
Protein-DNA contacts of the human interferon β enhancer
Ion channel activities translated to local movements on the protein energy landscape
Full-length Hsp70 protein
Molecular Biophysics Research Group
Understanding the molecular basis of biological processes is the goal of the Molecular Biophysics Research Group. In order to accomplish this objective, research teams use an interdisciplinary approach, coupling the methodologies and techniques of Structural and Computational Biology, with functional biochemical and biophysical assays to study the three dimensional structure, function, energetics and dynamics of macromolecules and macromolecular assemblies. Research interests are far-ranging and include mechanism of transcription, replication and recombination, signal transduction, membrane proteins and characterization of macromolecular machines. Two research laboratories focus on the structure determination of macromolecules using X-ray Crystallography, while recruitment in laboratories focusing in Nuclear Magnetic Resonance (NMR) and Electron Microscopy is ongoing. In addition, theoretical approaches are being extensively applied to research on protein biophysics. These methodologies often provide very useful explanations for experimental results and also exciting new hypothesis to test. Currently, the Computational Biology groups use mathematical methods at different levels ranging from quantum mechanics, molecular mechanics, to Langevin / Brownian dynamics, to study proteins with important physiological functions. Five research laboratories focus on understanding the function of ion channels and transporters in terms of molecular structure.
Dr. Meng Cui
Dr. Meng Cui’s research focuses on understanding the relationship between structure and function of membrane proteins, such as GPCRs and Ion channels. In this collaborative effort Dr. Cui utilizes computational modeling techniques, molecular mutagenesis and functional expression of the receptors and channels to understand the signal-recognition and transduction mechanism of these important macromolecules. By means of homology modeling, molecular docking, and molecular dynamics approaches, he seeks to understand how ligands or proteins interact and activate their receptors. Extensive long time molecular dynamics simulations based on coarse-grained models are being used to understand the ligand induced activation mechanism of ion channels. He is also developing computational approaches for loop modeling, flexible protein-ligand and protein-protein docking to achieve these goals.
Dr. Louis J. De Felice
A fluorescent probe (ASP+) in transit through the human serotonin transporter.
Dr. Louis J. De Felice and his laboratory focus on serotonin (5HT), dopamine (DA, and norepinephrine (NE) transporters. Serotonin transporters (SERTs), dopamine transporters (DATs), and NE transporters (NETs) are integral membrane proteins. Drugs, such as cocaine and antidepressants, act on neurotransmitter transporters and amphetamines and methamphetamines are taken up by neurons through these transporters, underlining the importance of these molecules on human behavior. Using cloned transporters transfected into host cells and native neuronal cells in tissue culture, De Felice and his group measure the ionic currents accompanying transport using two-microelectrode voltage clamp in frog oocytes and patch-clamp techniques on single mammalian cells. Cell-detached patches allow the lab to examine the kinetics of individual transporters, analogous to the study of single ion channels, and to study the regulation of transporters by ancillary proteins and small molecules. This information, in combination with classical radio-labeled uptake, amperometry, cell surface markers and correlative structural studies provide a comprehensive approach to the structure and function of neurotransmitter transporters.
Dr. Carlos R. Escalante
Research efforts in Dr. Carlos R. Escalante’s Structural Biology group are focused in the elucidation of the structure and molecular mechanisms of protein-DNA and protein-protein interactions that mediate transcriptional activation, viral DNA replication and recognition of bacterial pathogens by the innate immune system. The group uses X-ray crystallography in combination with Electron Microscopy (EM), Small Angle X-ray Scattering (SAXS) and other biophysical and biochemical techniques such as analytical ultracentrifugation (AUC) to obtain a complete structural and functional characterization of systems under study. We are particularly interested in complexes that assemble on the enhancers of the IFN-β gene and type I interferon stimulated genes required to activate transcription. In addition, we are studying the non-structural proteins of the Adeno-Associated Virus as archetypes of molecular motors involved in several DNA transactions such as DNA melting and unwinding and DNA packaging into viral capsids.
Dr. Qinglian Liu
Dr. Qinglian Liu and her group aim to understand the mechanism of protein folding and translocation, two essential processes in maintaining cellular protein homeostasis, which are facilitated by a major class of molecular chaperones, Hsp70. To understand the mechanism at atomistic level, we use X-ray crystallography to decipher the molecular architecture of Hsp70 at different states. Based on the structures, we then carry out biochemical and genetic analyses to complement the structural work. Another direction is related to Hsp40, a universal and essential activator of Hsp70. Since the molecular mechanism of this activation is poorly understood, we plan to use a similar multi-disciplinary approach to tackle this question, with the aid from additional biochemical and biophysical methods, such as surface plasmon resonance and fluorescence anisotropy. Maintaining protein homeostasis is essential for every cell; therefore, imbalance can lead to devastating disorders, such as neurodegenerative diseases and cancers. Based on the structural and functional studies, computational approaches will be applied to design novel therapeutic approaches for those diseases.
Dr. Diomedes E. Logothetis
Dr. Diomedes E. Logothetis and his group aim to understand ion channel regulation of gating in molecular terms. They are particularly interested in the regulation of ion channel activity by the βγ subunits of GTP-binding (G) proteins and by signaling phosphoinositides in the inner leaflet of the plasma membrane. Studies utilizing electrophysiology and molecular dynamic simulations are probing channel-PIP2 interactions. Post-translational modifications or protein-protein interactions regulate channel activity in a phosphoinositide-dependent manner and do so by targeting sites proximal to the channel-PIP2 amino acid residues. Ongoing studies are aiming to test the hypothesis that modulators of channel activity that depend on phosphoinositides work by adjusting channel-PIP2 interactions. The physiological implications of regulation of channel activity by G proteins and phosphoinositides is studied in model cells and also examined in cardiac and neuronal systems. Disease models of aberrant phoshoinositide regulation in transgenic animals and neuronal cell lines are being explored.
Dr. I. Scott Ramsey
Dr. I. Scott Ramsey studies proton-selective Hv1 and cation-nonselective TRP ion channels. Hv1 was identified by searching the mammalian genome for novel genes with homology to known voltage-gated channels. Hv1 contains an authentic voltage sensor domain but lacks a pore domain. Surprisingly, expression of Hv1 protein is sufficient to confer a proton conductance that essentially reconstitutes the hallmark biophysical properties of native voltage-gated H+ channels. Dr. Ramsey and his laboratory will use biophysical techniques to elucidate what may be a novel mechanism of ion transport. The cellular and physiological functions of Hv1 are being explored through the use of knockout mice. For example, proton channels may be important for innate immune responses to invading bacterial pathogens. After neutrophils engulf bacteria, they are believed to require a steady supply of protons to make the oxygen free radicals that help to kill the bugs and clear the infection. The laboratory will also investigate the roles of Hv1 in cells and tissues that are not primarily responsible for bacterial clearance. In parallel, the laboratory studies TRP channels, which are sensitive to myriad stimuli such as chemical ligands (e.g. calcium, menthol, capsaicin), thermal energy, electrical field strength, and interactions with both membrane lipids and channel-associated proteins. The lab is investigating gating, channel interactors and expression in a cell-specific context to decipher the molecular control and physiological consequences of TRP channel activity.
Dr. Gea-Ny Tseng
Dr. Gea-Ny Tseng and her group, including Dr. Min Jiang, are focusing on two interrelated projects. The first addresses structure-function relationships in cardiac voltage-dependent K (Kv) channels and the mechanism of action of pharmacological agents and dietary supplements. Studies of Kv channels seek to build three-dimensional models of delayed rectifier K channels (IKr, hERG; and IKs, KCNQ1/KCNE1) by combining mutagenesis and biophysical/biochemical analyses with computational methods. The second project investigates the mechanisms of ‘electrical remodeling’ in aging and diseased hearts and how the detrimental effects of electrical remodeling can be ameliorated by pharmacology agents and dietary supplements. Long-chain n-3 polyunsaturated fatty acids (PUFAs, found in fish oils) have been suggested to be protective in patients with heart disease, but there are indications that PUFAs may be detrimental in some cases. Presently the laboratory is characterizing the effects of PUFAs on cardiac electrical activity and remodeling in order to understand whether these agents are pro- or antiarrhythmic.
Dr. Lei Zhou
Dr. Lei Zhou and his group focus on the trilogy of structure-dynamics-function for ion channel proteins, specifically, the nature of correlated molecular motions as well as the corresponding changes in response to various external perturbations, such as membrane potential changes and ligand binding. This process begins when an external stimulus triggers changes in the funnel-like protein energy surface, accordingly, the distribution of protein conformation ensemble shifts from the resting state to the activated state. Current research evolves around the protein allostery of ion channels regulated by direct binding of a cyclic-nucleotide (cAMP or cGMP). A multidisciplinary approach including electrophysiology, biochemistry, and computational biology is being applied to test the hypothesis that ion channel’s function closely correlates with not only protein structure but more importantly with protein dynamics. Theoretical approaches being used include normal mode analysis (NMA) and principal component analysis (PCA). Furthermore, coarse-grained computational approaches are being developed to study the effect of surface structural water on protein dynamics.
