|
Research Interests
|
Our research
is aimed at applying theoretical and computational techniques to interesting
biophysical problems. We're especially interested in the class of membrane proteins
known as ion channels, which are essential for electrical and chemical
activity in all organisms and responsible for many neurological and
cardiovascular disorders. We aim to understand the microscopic driving forces
of protein function in cell membrane environments. Supported by: * NSF CAREER AWARD * * |
|
Thermodyamics of Ions and Ionizable groups in membranes Ionizable protein side chains play important roles in a wide array of biological phenomena, including: protein folding; protein-protein and protein-nucleic acid interactions; enzyme activity; pH activation of proteins; nuclear localization; peptide mediated membrane fusion; anti-microbial peptide activity; and various proton and ion transport mechanisms. The issue of ionizable protein side chains interacting with lipid membranes has been the focus of much attention since the proposal of the paddle model of voltage gated ion channels which suggested multiple arginine side chains may move through the hydrocarbon core of a lipid membrane, challenging a long standing view in membrane biophysics. We employ side chain analog and transmembrane helix models to determine the free energies of different ionizable protein side chains, as a function of protonation state, across membranes. Our findings have had implications for understanding the mechanisms of voltage gated ion channels and interpretations of translocon-based biological partitioning experiments. Download movie showing membrane deformations (4MB wmv format) |
|
|
Ab initio,
atomistic and coarse grained protein-lipid interactions Our membrane
simulations have revealed that lipid bilayers will deform due to the presence
of proteins, and especially charged solutes and protein side chains. This
leads to a complex solvation microenvironment for which empirical force fields
were not specifically parameterized.
We have employed model systems to attempt to match experimental bulk
partitioning and have carried out extensive quantum mechanical interaction
calculations for protein-lipid interactions.
Our findings demonatrate significant accuracy of free energy
calculations emerging from both empirical-additive models as well as
polarizable force field simulations.
In contrast, recent implementations of coarse-grained simulations of
protein-lipid interactions failed to reproduce the same structural changes in
lipid bilayers, exhibit interactions that are an order of magnitude too small
and subsequently lead to incorrect free energy profiles. |
|
|
Membrane Perturbations and Mismatch We have devised a series of projects employing
simple transmembrane segments as models of membrane proteins, as used
experimentally, to reveal general mechanisms of hydrophobic mismatch and its
effects on protein stability and function. Changes in structure and dynamics
of protein and lipids are examined and quantified thermodynamically by
performing umbrella sampling and alchemical free-energy calculations. |
|
|
| |
|
Role of lipid
composition on ion channel function In collaboration with Scott Feller ( |
|
|
Ionophore
membrane permeation We are exploring the mechanisms of natural ionophore permeation across
membranes using fully atomistic and continuum-based molecular dynamics
simulations. For example, valinomycin
is a neutral ionophore that is highly selective for potassium ions within lipid
bilayers and functions as an potassium-specific transporter; but the
microscopic details and thermodynamics underlying membrane permeability
remain largely unknown. |
|
|
Membrane protein conformational change Many
membrane proteins, including ion channels, undergo conformational changes in
transmembrane segments during activation.
These changes will be modulated by the composition of the membrane,
which consists of a bilayer arrangement of up to 200 different species of
lipid, as well as amphiphilic molecules, proteins and pharmacological agents
that can affect membrane mechanical and electrostatic properties. We are developing microscopic models to
elucidate the general mechanical and electrostatic mechanisms of ion channel
regulation in cell membranes by using free energy simulation methods to
examine modulated protein conformational change. The ability to
quantitatively predict and explain the effects of modifying agents on protein
activity will represent a significant advance in computational biophysics. |
|
|
Ion channel
selectivity and blocking mechanisms In collaboration with Crina Nimigean (Cornell) we
have been investigating mechanisms of ion selectivity and blocking in
potassium channels using electrophysiology and MD simulation. The highly
conserved pore region of these channels is very selective for potassium, due
to a series of backbone carbonyls projecting into the ion permeation
pathway. Dehydration of smaller
monovalent cations, such as sodium and lithium, is, however, highly
unfavorable. Experimental studies
reveal blocking by these smaller ions, yet also reveal interesting features
at higher membrane voltages. |
|
|
Electrostatics
of supported bilayers In collaboration with Atul Parikh (Applied Science)
we have been exploring experimental and computational methods to quantify the
asymmetric distribution of charged molecules between the leaflets of
solid-substrate-supported phospholipid bilayers. On silica surfaces, negatively charged
lipid components are shown to be enriched in the outer leaflet of a supported
bilayer system at modest salt concentrations. The approaches developed
provide a general means for exploring asymmetries of charged components in
supported bilayer systems. |
|
|
Calcium binding
proteins in vision In collaboration with Jim Ames (Chemistry), we are
combining NMR and MD simulations to understand the function of the calcium
sensor protein Recoverin involved in vision.
We are currently using biased trajectory simulation methods to study
the conformational changes of this protein upon calcium binding that lead to
the protrusion of a Myr group that promotes membrane binding. |
|
|
Ion channel permeation We have employed free energy techniques for understanding permeation and valence selectivity of narrow ion channels. We have explored permeation mechanisms by extracting multi-dimensional PMFs as a function of ion position, solvation and water alignment and have found semi-quantitative agreement with experimental conductance and binding measurements. We have been investigating the role of the protein in stabilizing different ions and the limitations of MD force-fields for modeling these extremely challenging process. Permeation GIF Download |
|
|
Effects of protein thermal fluctuations on ion permeation: Atomic structures of proteins, including ion channels, usually are depicted as static entities. This provides for a convenient representation of the proteins overall structure, but at the risk of deemphasizing the importance of thermal fluctuations in the protein function.These fluctuations become particularly important in narrow pores. Descriptions of ion permeation which employ static protein structures and a macroscopic continuum dielectric solvent face significant difficulties. Download Movie Showing Fluctuations (6MB mpeg format)
|
|
|
MD as a tool for NMR protein structural refinement Solid-state NMR has become increasingly important for investigating the structure of membrane proteins. Microscopic models incorporating a realistic molecular environment can be used to generate a dynamic ensemble that reproduces experimental observations with remarkable precision. Our results demonstrate that MD is a powerful tool for membrane protein structural refinement.
|
|
|
Methodological improvements Slow
movement of lipid molecules in a bilayer poses a difficulty for investigating
protein function. We're developing improved sampling techniques that combine
umbrella sampling and |
|