Marcela Madrid

Refined solution structure and ligand-binding properties of PDC-109 domain b. A collagen-binding type II domain.

We have determined, via 1H-n.m.r., the solution conformation of the collagen-binding b-domain of the bovine seminal fluid protein PDC-109 (PDC-109/b). The structure determination is based on 341 interproton distance estimates and 42 dihedral angle estimates: a set of 24 initial structures were computed; 12 using the variable target function program DIANA, and 12 using the metric matrix program DISGEO. These structures were optimized by restrained energy minimization and dynamic simulated annealing using the CHARMM and X-PLOR programs. The average pairwise root-mean-square difference (r.m.s.d) between the optimized DIANA (DISGEO) structures is 0.71 A (0.82 A) for the backbone atoms, and 1.73 A (2.03 A) for all atoms. Both sets of structures exhibit the same global fold, secondary structure and placement of most non-polar side-chains. Two central antiparallel beta-sheets, which lie roughly perpendicular to each other, and two irregular loops support a large, partially exposed, hydrophobic surface that defines a putative binding site. A test of a hybrid relaxation matrix-based distance refinement protocol (MIDGE program) was performed using a normalized 250 millisecond NOESY spectrum. The resulting distances were input to the molecular mechanics/dynamics procedures mentioned above in order to optimize the DIANA structures. Our results indicate that relaxation matrix refinement of distances is most useful when used conservatively for identifying underestimated distance constraints. 1H-n.m.r. monitored ligand titration experiments revealed definite, albeit weak, binding interactions for phenethylamine and leucine analogs (Ka less than or equal to 25 M-1). Residues perturbed by ligand binding include Tyr7, Trp26, Tyr33, Asp34 and Trp39. These results suggest that PDC-109/b may recognize specific leucine and/or isoleucine-containing sequences within collagen.

In-Plane and Out-Of-Plane Thermal Conductivity of Silicon Thin Films Predicted by Molecular Dynamics

The thermal conductivity of silicon thin films is predicted in the directions parallel and perpendicular to the film surfaces (in-plane and out-of-plane, respectively) using equilibrium molecular dynamics, the Green-Kubo relation, and the Stillinger-Weber interatomic potential. Three different boundary conditions are considered along the film surfaces: frozen atoms, surface potential, and free boundaries. Film thicknesses range from 2 to 217 nm and temperatures from 300 to 1000 K. The relation between the bulk pho.-non mean free path (A) and the film thickness (d s ) spans from the ballistic regime (A ≥ d s ) at 300 K to the diffusive, bulk-like regime (Λ «d s ) at 1000 K. When the film is thin enough, the in-plane and out-of-plane thermal conductivity differ from each other and decrease with decreasing film thickness, as a consequence of the scattering of phonons with the film boundaries. The in-plane thermal conductivity follows the trend observed experimentally at 300 K. In the ballistic limit, in accordance with the kinetic and phonon radiative transfer theories, the predicted out-of-plane thermal conductivity varies linearly with the film thickness, and is temperature-independent for temperatures near or above the Debyes temperature.

Molecular dynamics simulations of a fully hydrated dimyristoylphosphatidylcholine membrane in liquid-crystalline phase

Molecular dynamics (MD) simulations were performed to investigate the structure of a fully hydrated 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) bilayer in liquid-crystalline (fluid) phase at 30 °C. The bilayer consists of 200 DMPC lipid molecules with nw=27.4 water molecules per lipid. The membrane was built with reference to the coordinates of a previously published 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membrane patch. A four-step dynamic procedure (110 ps) with Berendsen pressure rescaling (P=0 and 1 bar), applied in all three directions, was used to rapidly prepare the bilayer. This system was then subjected to two separate constant pressure and temperature simulations at 1 bar and 30 °C for ∼380 ps, using the Nose–Hoover NPT method with periodical boundaries and Berendsen temperature and pressure rescaling method, respectively. The resultant bilayer has an area per lipid of 59.2 A2 and a head-to-head thickness (DHH) of 36.3 A. These values are in good agreement with the x-ray ...

Thermal Properties for Bulk Silicon Based on the Determination of Relaxation Times Using Molecular Dynamics

Molecular dynamics simulations are performed to estimate acoustical and optical phonon relaxation times, dispersion relations, group velocities, and specific heat of silicon needed to solve the Boltzmann transport equation (BTE) at 300 K and 1000 K. The relaxation times are calculated from the temporal decay of the autocorrelation function of the fluctuation of total energy of each normal mode in the ⟨100⟩ family of directions, where the total energy of each mode is obtained from the normal mode decomposition of the motion of the silicon atoms over a period of time. Additionally, silicon dispersion relations are directly determined from the equipartition theorem obtained from the normal mode decomposition. The impact of the anharmonic nature of the potential energy function on the thermal expansion of the crystal is determined by computing the lattice parameter at the cited temperatures using a NPT (i.e., constant number of atoms, pressure, and temperature) ensemble, and are compared with experimental values reported in the literature and with those computed analytically using the quasiharmonic approximation. The dependence of the relaxation times with respect to the frequency is identified with two functions that follow the functional form of the relaxation time expressions reported in the literature. From these functions a simplified version of relaxation times for each normal mode is extracted. Properties, such as group and phase velocities, thermal conductivity, and mean free path, needed to further develop a methodology for the thermal analysis of electronic devices (i.e., from nano- to macroscales) are determined once the relaxation times and dispersion relations are obtained. The thermal properties are validated by comparing the BTE-based thermal conductivity against the predictions obtained from the Green–Kubo method. It is found that the relaxation times closely resemble the ones obtained from perturbation theory at high temperatures; the contribution to the thermal conductivity of the transverse acoustic, longitudinal acoustic, and longitudinal optical modes being approximately 30%, 60%, and 10%, respectively, and the contribution of the transverse optical mode negligible.

Solution structure of a peptide nucleic acid duplex from NMR data: features and limitations.

This paper describes the results of a 1D and 2D NMR spectroscopy study of a palindromic 8-base pair PNA duplex GGCATGCC in H2O and H2O-D2O solutions. The (1)H NMR peaks have been assigned for most of the protons of the six central base pairs, as well as for several amide protons of the backbone. The resulting 36 interbase and base-backbone distance restraints were used together with Watson-Crick restraints to generate the PNA duplex structure in the course of 10 independent simulated annealing runs followed by restrained molecular dynamics (MD) simulations in explicit water. The resulting PNA structures correspond to a P-type helix with helical parameters close to those observed in the crystal structures of PNA. Based on the current limited number of restraints obtained from NMR spectra, alternative structures obtained by MD from starting PNA models based on DNA cannot be ruled out and are also discussed.

Model-independent refinement of interproton distances generated from 1H NMR overhauser intensities

A recursive method to refine interproton distances compatible with two-dimensional nuclear Overhauser effect (NOESY) experiments has been tested. Convergence does not depend on the initial estimate of the parameters. Hence, no approximate initial structure of the molecule is required: the iterative process can be started from the experimentally measured NOESY cross-peak volumes, supplemented with arbitrary cross-peak and autopeak values to obtain an initial NOESY matrix. The relaxation matrix is calculated from the NOESY matrix, and its diagonal elements (ϱi) are adjusted at each iteration until the difference between theoretical and experimental cross peaks is a minimum. The improvement comes from using interproton distances calculated from the off-diagonal (σij) elements to generate ϱi values. The method was applied to alumichrome, a rigid cyclohexapeptide of virtually identical solution and crystallographic structures. The experimental data consisted of the integrated volumes of NOESY cross peaks at 500 MHz. Convergence was tested by resorting to different initial conditions, one of them being a NOESY matrix in which the experimentally unobserved off diagonal elements were set equal to zero and the diagonal elements to 0.5. The iterations rapidly converge, in all cases, to a set of distances whose root-mean-squares deviation (rmsd) from the crystallographic distances is < 0.05 A. The acronym MIDGE (model-independent distance generation) for the procedure is proposed.

Molecular dynamics of HIV‐1 reverse transcriptase indicates increased flexibility upon DNA binding

HIV‐1 reverse transcriptase (RT) is one of the main targets for drugs used in the treatment of AIDS, among them, the non‐nucleoside RT inhibitors (NNRTIs). The flexibility of RT unliganded and complexed to double‐stranded DNA (RT/dsDNA), in water, has been studied by means of molecular dynamics. The simulations show that RT flexibility depends on its ligation state. The RT/dsDNA trajectories show larger fluctuations in the atomic positions than uncomplexed RT, particularly at the tips of the p66 fingers and thumb subdomains. This increased flexibility is consistent with the ability of the p66 fingers of the RT/dsDNA complex to close down after the binding of a deoxynucleoside triphosphate (dNTP) molecule, as observed in the crystal structures of RT/dsDNA bound to dNTP. The two complexation states present different patterns of concerted motions, indicating that the bound dsDNA alters RT flexibility. The motions of amino acid residues that form the non‐nucleoside RT inhibitor binding pocket upon complexation with a NNRTI are anticorrelated with the p66 fingers (in RT/dsDNA) and correlated to the RNase H subdomain (unliganded RT). These concerted motions indicate that binding of a NNRTI could alter the flexibility of the subdomains whose motions are correlated to those of the binding pocket. Proteins 2001;45:176–182.

Consequences of magnetization transfer on the determination of solution structures of proteins

Abstract The complete two-dimensional nuclear Overhauser enhancement (NOESY) spectra of several proteins were theoretically simulated to analyze the effect that spin diffusion has on the cross-peak intensity-interproton distance relationship as a function of rotational time τ and mixing time tm. The NOESY cross-peak intensities were calculated by solving the generalized Bloch equations from the crystal coordinates of basic pancreatic trypsin inhibitor, cytochrome b562, domain 1 of phage lysozyme, and human deoxy hemoglobin (MW 6500, 11,459, 18,625, and 64,450, respectively). It was found that correlations between cross-peak intensity and internuclear distance, useful for obtaining solution structure of proteins from nuclear magnetic resonance data, can be defined for cross peaks observed at tm = 100 ms, for rotational correlation times τ

Effect of Backbone Flexibility on Charge Transfer Rates in Peptide Nucleic Acid Duplexes

Charge transfer (CT) properties are compared between peptide nucleic acid structures with an aminoethylglycine backbone (aeg-PNA) and those with a γ-methylated backbone (γ-PNA). The common aeg-PNA is an achiral molecule with a flexible structure, whereas γ-PNA is a chiral molecule with a significantly more rigid structure than aeg-PNA. Electrochemical measurements show that the CT rate constant through an aeg-PNA bridging unit is twice the CT rate constant through a γ-PNA bridging unit. Theoretical calculations of PNA electronic properties, which are based on a molecular dynamics structural ensemble, reveal that the difference in the CT rate constant results from the difference in the extent of backbone fluctuations of aeg- and γ-PNA. In particular, fluctuations of the backbone affect the local electric field that broadens the energy levels of the PNA nucleobases. The greater flexibility of the aeg-PNA gives rise to more broadening, and a more frequent appearance of high-CT rate conformations than in γ-PNA.

Major subdomain rearrangement in HIV-1 reverse transcriptase simulated by molecular dynamics

We have performed eight 1‐ns in vacuo molecular dynamics simulations of HIV‐1 reverse transcriptase (RT). Starting with the p66 thumb subdomain in an upright configuration, the p66 thumb moved down over the palm during six of the eight trajectories, in excellent agreement with the crystallographic structure of unliganded RT. The large rearrangement of the p66 thumb subdomain, its tip moving approximately 30 Å, occurs during the first 30‐200 ps. This approach may allow a detailed study of the processes involved in biologically significant conformational changes in macromolecules. Proteins 1999;35:332–337.