Biomedical subjects

Frank Suits

Publications and source records attributed to Frank Suits.

5 recordsLinked to original sources

PubMed2006

The roaming atom pathway in formaldehyde decomposition.

We present a detailed experimental and theoretical investigation of formaldehyde photodissociation to H(2) and CO following excitation to the 2(1)4(1) and 2(1)4(3) transitions in S(1). The CO velocity distributions were obtained using dc slice imaging of single CO rotational states (v=0, j(CO)=5-45). These high-resolution measurements reveal the correlated internal state distribution in the H(2) cofragments. The results show that rotationally hot CO (j(CO) approximately 45) is produced in conjunction with vibrationally "cold" H(2) fragments (v=0-5): these products are formed through the well-known skewed transition state and described in detail in the accompanying paper. After excitation of formaldehyde above the threshold for the radical channel (H(2)CO-->H+HCO) we also find formation of rotationally cold CO (j(CO)=5-28) correlated to highly vibrationally excited H(2) (v=6-8). These products are formed through a novel mechanism that involves near dissociation followed by intramolecular H abstraction [D. Townsend et al., Science 306, 1158 (2004)], and that avoids the region of the transition state entirely. The dynamics of this "roaming" mechanism are the focus of this paper. The correlations between the vibrational states of H(2) and rotational states of CO formed following excitation on the 2(1)4(3) transition allow us to determine the relative contribution to molecular products from the roaming atom channel versus the conventional molecular channel.

Carbon Monoxide↗

PubMed2005

Molecular dynamics investigation of the structural properties of phosphatidylethanolamine lipid bilayers.

We report a 14 ns microcanonical (NVE) molecular dynamics simulation of a fully hydrated bilayer of 1-stearoyl-2-oleoyl-phosphatidyethanolamine. This study describes the structure of the bilayer in terms of NMR order parameters and radial distribution functions, and compares them to experimental results and simulations of other lipids. A focus of this work is the characterization of the lipid-water interface, particularly the hydrogen bonding network of the phosphatidylethanolamine (PE) headgroups. We find that hydrogen bonding between the primary amine and phosphate groups has a pronounced effect on the structure of PE relative to phosphatidylcholine, and is evident in, for example, the P-N radial distribution functions.

Amines↗

PubMed2005

Molecular dynamics investigation of dynamical properties of phosphatidylethanolamine lipid bilayers.

We describe the dynamic behavior of a 1-stearoyl-2-oleoyl-phosphatidylethanolamine (SOPE) bilayer from a 20 ns molecular dynamics simulation. The dynamics of individual molecules are characterized in terms of (2)H spin-lattice relaxation rates, nuclear overhauser enhancement spectroscopy (NOESY) cross-relaxation rates, and lateral diffusion coefficients. Additionally, we describe the dynamics of hydrogen bonding through an analysis of hydrogen bond lifetimes and the time evolution of clusters of hydrogen bonded lipids. The simulated trajectory is shown to be consistent with experimental measures of internal, intermolecular, and diffusive motion. Consistent with our analysis of SOPE structure in the companion paper, we see hydrogen bonding dominating the dynamics of the interface region. Comparison of (2)H T(1) relaxation rates for chain methylene segments in phosphatidylcholine and phosphatidylethanolamine bilayers indicates that slower motion resulting from hydrogen bonding extends at least three carbons into the hydrophobic core. NOESY cross-relaxation rates compare well with experimental values, indicating the observed hydrogen bonding dynamics are realistic. Calculated lateral diffusion rates (4 +/ -1 x 10(-8) cm(2)s) are comparable, though somewhat lower than, those determined by pulsed field gradient NMR methods.

Algorithms↗

PubMed2005

Role of cholesterol and polyunsaturated chains in lipid-protein interactions: molecular dynamics simulation of rhodopsin in a realistic membrane environment.

We present a 118-ns molecular dynamics simulation of rhodopsin embedded in a bilayer composed of a 2:2:1 mixture of 1-stearoyl-2-docosahexaenoyl-phosphatidylcholine (SDPC), 1-stearoyl-2-docosahexaenoyl-phosphatidylethanolamine (SDPE), and cholesterol, respectively. The simulation demonstrates that the protein breaks the lateral and transverse symmetry of the bilayer. Lipids near the protein preferentially reorient such that their unsaturated chains interact with the protein, while the distribution of cholesterol in the membrane complements the variations in rhodopsin's transverse profile. The latter phenomenon suggests a molecular-level mechanism for the experimental finding that cholesterol stabilizes the native dark-adapted state of rhodopsin without binding directly to the protein.

Cholesterol↗

PubMed2004

Molecular-level organization of saturated and polyunsaturated fatty acids in a phosphatidylcholine bilayer containing cholesterol.

Cholesterol's preference for specific fatty acid chains is investigated at the atomic level in a 20 ns molecular dynamics computer simulation of a lipid bilayer membrane consisting of cholesterol and 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (SDPC) in a 1:3 ratio. These simulations reproduce experimental measurements suggesting that cholesterol prefers to be solvated by saturated acyl chains and has a low affinity for polyunsaturated fatty acids. Analyses of the simulation trajectory provide a detailed picture of both the transverse and lateral structures of the lipid bilayer membrane, along with a description of lipid and cholesterol dynamics at high temporal resolution. Comparison with a previous simulation of a pure phospholipid bilayer allows an atomic-level description of the changes in membrane structure and dynamics resulting from incorporation of cholesterol. The observed differential cholesterol interactions with saturated and polyunsaturated lipids provide a mechanism for the formation of laterally inhomogeneous membranes; thus, the simulation provides molecular-level insight into the formation of lipid rafts.

Cholesterol↗