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Written by Linda Prengaman
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Tuesday, 03 June 2008 |
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Ion channels play an important role in excitable cells such
as neurons. Because dysfunctions of ion
channels in such cells can wreak havoc on an organism, we seek to develop
accurate models of ion channel behavior.
This work focuses on the narrow channel Gramicidin A, which conducts
mainly monovalent cations. A gramicidin
A channel containing one cation and several water molecules was inserted into a
DMPC lipid bilayer containing 128 lipids. Left: Gramicidin A channel (green) with K+ ion (pink), solvated
in DMPC lipid bilayer (gray)
Torsion parameters for the DMPC bilayer in the AMBER9 software package were
developed by our group. The behaviors of
four cations, Li+, Na+, K+, and Cs+, in the channel were examined. After a series of molecular dynamics (MD)
simulations to equilibrate the system using PMEMD, a part of the AMBER9
software package, the electrostatic free energy of the system was
calculated. This provided an energy
profile for each ion as it passed through the channel. According to preliminary results, a temporary
binding site for all four cations approximately 9Å from the center of the
channel was identified. In the future, we hope to use thermodynamic integration to more closely
examine the difference between the cations, especially in places where the
electrostatic energy wildly differs from cation to cation.
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Last Updated ( Tuesday, 03 June 2008 )
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Written by Mike
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Monday, 02 June 2008 |
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Investigating the role of electrostatic interactions
in Glutamate receptor mechanism by multi-scale theoretical modeling.
Elevated levels of glutamate during cerebral ischemia
play a major role in excitotoxicity of glutamate receptors (GluRs) leading to
neuron death and devastating effects on the central nervous system. Studies
show that antagonists of the AMPA GluR subtype have a neuroprotective effect on
a variety of ischemic models. Functional diversity of GluR in the brain is
revealed in clinical trials showing antagonists produce such side effects as
developmental dysfunction and psychosis. Clearly understanding the mechanism by
which GluRs function is critical for rational drug design which may provide
neuroprotection over antagonists of the receptor. Modeling the conformational change in S1-S2
that occurs upon ligand binding indicate the ligand bound conformation may be
stabilized by hydrogen bonding and long-range electrostatic attraction.
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Last Updated ( Monday, 02 June 2008 )
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Written by Jose Christian Flores Canales
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Monday, 02 June 2008 |
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 Membrane
proteins represent almost 30% of all proteins in most sequenced genomes.
However, membrane proteins represent less than 1% of the total number of
protein structures in the PDB server. Among the reasons of this dissimilar
distribution, it is the arduous crystallization process of membrane proteins. Crystallization process must preserve the complex structure-function
relationship between membrane proteins and the anisotropic environment of
membrane lipids. Based on known structures and secondary domain prediction
methods, it is possible to determine two common motifs on membrane proteins: alpha-helix
and β-barrel.
Our aim is to predict the structure of helical membrane proteins
based on a coarse grained model, residue-residue energy interactions and conformational
sampling methods. The coarse grained model is based on a rigid body representation
of transmembrane alpha-helices bundles. To model the alpha-helix packing interactions
in the membrane surface we use a statistical residue-residue free energy of
interaction. In order to explore effectively the helix packing space we employ methods
such as Monte Carlo and
Geometrical Simulation techniques.
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Last Updated ( Thursday, 12 June 2008 )
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Written by Larry Layne
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Wednesday, 21 May 2008 |
 The Na+/H+ exchange regulating factor-1 (NHERF) acts as a scaffold between transmembrane GPCR proteins, such as β2 adrenergic, platelet-derived growth factor, and parathyroid hormone receptors, and the actin of the cytoskeleton. There are three binding domains contained within the NHERF-1; PDZ-1, PDZ-2, and ERM. While the ERM domain binds the NHERF-1 and the cytoskeleton, the main thrust of our research is concerned with the binding of PDZ-1, which connects the transmembrane GPCRs with the NHERF-1. Each of the different receptors that bind to the NHERF has a different collection of four C-terminus peptides that bind to the PDZ-1 binding domain. An attempt is being made to determine which sequence of peptides binds preferentially to the PDZ-1. This preferential sequence will then act as a template for the design of a ligand. This ligand will have a greater binding affinity then the parent peptide sequence and should subsequently displace any native sequence in vitro and theoretically, in vivo. The experimental aspects of this project are being done in conjunction with the Friedman group and the Romero group, both part of the University of Pittsburgh’s Department of Pharmacology and Chemical Biology.
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Last Updated ( Wednesday, 21 May 2008 )
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Written by Kolya
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Monday, 19 May 2008 |
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Ionotropic Glutamate Receptors (GluRs) are ligand-gated transmembrane ion channels mainly
responsible for fast excitatory synaptic signaling in brain. GluRs are segregated into three
subtypes according to their sensitivity to agonists (ligands) AMPA, kainite or NMDA. Ligands
bind to an extracellular domain of receptor subunits, which causes receptor activation rapidly
followed by a desensitized state (inactive state).
We study mechanisms of receptor-ligand interaction, receptor activation and ion
permeation in glutamate receptor ion channels. To understand the receptor activation process one
first needs to build a model of molecular basis for the apparent differences in the GluRs binding
mode to various ligands (glutamate, AMPA, kainite, DNQX). We are currently studying
ligand-protein vibrational modes, electrostatical interations in the binding site and periphery of
the protein, role of bound water in the protein binding site as well as bioinformatics approaches to
the construction of the intact receptor to achieve this goal.
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Last Updated ( Tuesday, 03 June 2008 )
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Read more...
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Written by Tatyana Mamonova
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Monday, 19 May 2008 |
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 We are interested in understanding the mechanism of alpha-hemolysin ion-channel, a bacterial toxin that forms a heptametric transmembrane pore in the form of beta-barrel. alpha-Hemolysin (aHL) has several characteristics that make it particularly attractive for biomolecular engineering and design. Some possible applications for aHL include biosensor elements capable of sequencing DNA, a variety of sensors for specific chemicals in solution, building an aray of nanopores with controlled dimentions etc. We compute ion current through the alpha-hemolysin channel using continuum electrostatics drift-diffusion theory PNP (link!) and its hierarchical modification PMFPNP (make it link!) Our goal is to understand how the protein structure affects its function. For example, at varying pH levels of the surrounding solution conduction properties of the channel are different.
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Last Updated ( Tuesday, 20 May 2008 )
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Written by Tatyana Mamonova
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Monday, 19 May 2008 |
 The main goal of this project is to study interaction between the transmembrane pore protein a-hemolysin (aHL) and the cyclic oligosaccharide b-cyclodextrin (bCD). bCD belongs to the family of cyclodextrins, able to form host-guest complexes with a variety of organic moleculars. We consider the a-hemolysin channel as an example in which the guest molecule enters the aHL channel site thus modifying its conductance of simple ions. The host-guest configuration of the complex and the nature of the binding are not known. For detailed understanding of the mechanisms of intermolecular interaction in such complexes we have performed a large-scale molecular dynamics simulation of b-cyclodextrin confined inside the lumen of the a-hemolisin channel. Our preliminary results demonstrate that the configurations of the system with bCD near Met-113 are characterized by the most negative interaction and binding energies. We will perform the comparison of bCD free energy of binding with aHL with modified amino-acids via free energy techniques and assess the influence of the modification of the channel structure on channel adaptor binding energy and adaptor residence time.
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Last Updated ( Tuesday, 20 May 2008 )
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Research 
