Biomedical subjects

M Parrinello

Publications and source records attributed to M Parrinello.

At least 19 recordsLinked to original sources

PubMed2001

Ab initio molecular dynamics-based assignment of the protonation state of pepstatin A/HIV-1 protease cleavage site.

A recent 13C NMR experiment (Smith et al. Nature Struct. Biol. 1996, 3, 946-950) on the Asp 25-Asp25' dyad in pepstatin A/HIV-1 protease measured two separate resonance lines, which were interpreted as being a singly protonated dyad. We address this issue by performing ab initio molecular dynamics calculations on models for this site accompanied by calculations of 13C NMR chemical shifts and isotopic shifts. We find that already on the picosecond time-scale the model proposed by Smith et al. is not stable and evolves toward a different monoprotonated form whose NMR pattern differs from the experimental one. We suggest, instead, a different protonation state in which both aspartic groups are protonated. Despite the symmetric protonation state, the calculated 13C NMR properties are in good agreement with the experiment. We rationalize this result using a simple valence bond model, which explains the chemical inequality of the two C sites. The model calculations, together with our calculations on the complex, allow also the rationalization of 13C NMR properties on other HIV-1 PR/inhibitor complexes. Both putative binding of the substrate to the free enzyme, which has the dyad singly protonated (Piana, S.; Carloni, P. Proteins: Struct., Funct., Genet. 2000, 39, 26-36), and pepstatin A binding to the diprotonated form are consistent with the inverse solvent isotope effect on the onset of inhibition of pepsin by pepstatin and the kinetic iso-mechanism proposed for aspartic proteases (Cho, T.-K.; Rebholz, K.; Northrop, D.B. Biochemistry 1994, 33, 9637-9642).

Aspartic Acid↗

PubMed2001

Action-derived molecular dynamics in the study of rare events.

We present a practical method to generate classical trajectories with fixed initial and final boundary conditions. Our method is based on the minimization of a suitably defined discretized action. The method finds its most natural application in the study of rare events. Its capabilities are illustrated by nontrivial examples. The algorithm lends itself to straightforward parallelization, and when combined with ab initio molecular dynamics it promises to offer a powerful tool for the study of chemical reactions.

Algorithms↗

PubMed2001

Autoionization in liquid water.

The dissociation of a water molecule in liquid water is the fundamental event in acid-base chemistry, determining the pH of water. Because of the short time scales and microscopic length scales involved, the dynamics of this autoionization have not been directly probed by experiment. Here, the autoionization mechanism is revealed by sampling and analyzing ab initio molecular dynamics trajectories. We identify the rare fluctuations in solvation energies that destabilize an oxygen-hydrogen bond. Through the transfer of protons along a hydrogen bond "wire," the nascent ions separate by three or more neighbors. If the hydrogen bond wire connecting the two ions is subsequently broken, a metastable charge-separated state is visited. The ions may then diffuse to large separations. If, however, the hydrogen bond wire remains unbroken, the ions recombine rapidly. Because of their concomitant large electric fields, the transient ionic species produced in this case may provide an experimentally detectable signal of the dynamics we report.

Journal Article↗

PubMed2001

Structural and electronic properties of Co-corrole, Co-corrin, and Co-porphyrin.

A quantitative study of the structure and electronic properties of Co-corrole, Co-corrin, and Co-porphyrin, using density functional theory, is reported. The structure of each macrocycle is optimized, with no symmetry constraints, by considering different spin states. The ground-state structures and spin states (S = 1 for Co-corrole, S = 0 for Co-corrin and S = 1/2 for Co-porphyrin) are in good agreement with the experimental data available. The trends in the sizes of the coordination cavities upon varying the inner metal atom and/or the macrocycle are analyzed and compared with those for the Fe-porphyrin we studied previously. Our results reveal that most of the distortion of the Co-corrin core in the B12 coenzyme is due to the inherent properties of Co-corrin. Quite different behaviors are found between corrinoids and porphyrins upon varying the spin state. While an increase in the metal-nitrogen (M-N) distance with spin state occurs in the porphyrins, the corrinoids show little variation in the M-N distance and, in some cases, undergo small structural changes in the ring structure. These results aid in understanding the often discussed question of why nature has chosen corrin/porphyrin for carrying out the particular biological functions identified in the B12 coenzyme.

Cobalt↗

PubMed2001

Influence of the heme pocket conformation on the structure and vibrations of the Fe-CO bond in myoglobin: a QM/MM density functional study.

The influence of the distal pocket conformation on the structure and vibrations of the heme-CO bond in carbonmonoxy myoglobin (MbCO) is investigated by means of hybrid QM/MM calculations based on density functional theory combined with a classical force field. It is shown that the heme-CO structure (QM treated) is quite rigid and not influenced by the distal pocket conformation (MM treated). This excludes any relation between FeCO distortions and the different CO absorptions observed in the infrared spectra of MbCO (A states). In contrast, both the CO stretch frequency and the strength of the CO...His64 interaction are very dependent on the orientation and tautomerization state of His64. Our calculations indicate that the CO...N(epsilon) type of approach does not contribute to the A states, whereas the CO...H-N(epsilon) interaction is the origin of the A(1) and A(3) states, the His64 residue being protonated at N(epsilon). The strength of the CO...His64 interaction is quantified, in comparison with the analogous O(2)...His64 interaction and with the observed changes in the CO stretch frequency. Additional aspects of the CO...His64 interaction and its biological implications are discussed.

Carbon Monoxide↗

PubMed2000

Solvation of radical cations in water--reactive or unreactive solvation?

The solvation and reaction of ethylene radical cation in aqueous solution has been studied with Car-Parrinello molecular dynamics simulations. All ab initio simulations were performed using a system of 56 water and one ethylene molecule. Using a favorable symmetrically solvated radical cation as the starting point of the simulation a fast addition of water (within 90 fs) to the radical cation is observed. The primary addition product is rapidly deprotonated (within 100 fs) to yield the ethanol-2-yl radical. A second simulation was initiated through vertical ionization of neutral hydrated ethylene, representing a significantly less favorable situation for the addition process. No addition of water can be observed in this second simulation over a time span of 1.7 ps. Taken together the two simulations are indicative of a rearrangement of the solvent shell which represents the major part of the overall reaction barrier. Under these circumstances, the reaction rate of an otherwise spontaneous reaction is limited by the intrinsic solvent relaxation time. This interpretation of the reactivity of hydrated radical cations reconciles previously conflicting experimental condensed phase and theoretical gas phase studies.

Journal Article↗

PubMed2000

Hydrogen bonding and dipole moment of water at supercritical conditions: a first-principles molecular dynamics study.

We present a first-principles molecular dynamics study of water near and above the critical point ( T = 647 K, rho = 0.32 g/cm(3)). We find that the systems undergo fast dynamics with continuous formation and breaking of H bonds. At low density, the system fragments mostly into trimers, dimers, and single molecules. At a higher density, more complex structures appear and an extended, albeit very dynamical, H-bond network can be identified. These structures have important consequences for the screening properties of the system. This offers a clue to understanding the peculiar chemical behavior of a supercritical system and allows thermodynamical tuning of its solvent properties.

Journal Article↗

PubMed2000

Ab initio simulation of phase transitions and dissociation of H2S at high pressure

By ab initio constant pressure molecular dynamics, we have identified the structure of phase V and phase VI of H2S at 35 and 65 GPa, respectively. The theoretical IR spectra of both phases are consistent with experimental findings and support our proposed structural models. We find that phase V is characterized by the presence of charged SH+3 and SH- species which are created and destroyed dynamically, whereas phase VI is no longer a molecular phase but consists of sheets of S with the majority of H intercalated between the layers. The stability of the two phases with respect to dissociation into elemental crystalline hydrogen and sulfur is discussed.

Journal Article↗

PubMed2000

Two-membered silicon rings on the dehydroxylated surface of silica

We present extensive modeling of the amorphous silica surface, aimed at connecting its structural and chemical features. beta-cristobalite surfaces are initially studied to model the hydroxylated surfaces. A model reconstruction of the (111) surface is used to define a path leading to the formation of two-membered silicon rings upon dehydroxylation. Subsequently, a realistic model of the amorphous dehydroxylated (dry) surface is produced, by full ab initio annealing of an initial model generated by classical simulation. The presence of surface two-membered silicon rings emerges naturally. A calculation of IR activity yields an associated peak doublet in agreement with experimental data.

Journal Article↗

PubMed2000

Ab initio molecular dynamics with a classical pressure reservoir: simulation of pressure-induced amorphization in a Si35H36 cluster

We present a new constant-pressure ab initio molecular dynamics method suitable for studying, e.g., pressure-induced structural transformations in finite nonperiodic systems such as clusters. We immerse an ab initio treated cluster into a model classical liquid, described by a soft-sphere potential, which acts as a pressure reservoir. The pressure is varied by tuning the parameter of the liquid potential. We apply the method to a Si35H36 cluster, which undergoes a pressure-induced amorphization at approximately 35 GPa, and remains in a disordered state even upon pressure release.

Journal Article↗

PubMed2000

A comparative study of galactose oxidase and active site analogs based on QM/MM Car-Parrinello simulations.

A parallel study of the radical copper enzyme galactose oxidase (GOase) and a low molecular weight analog of the active site was performed with dynamical density functional and mixed quantum-classical calculations. This combined approach enables a direct comparison of the properties of the biomimetic and the natural systems throughout the course of the catalytic reaction. In both cases, five essential forms of the catalytic cycle have been investigated: the resting state in its semi-reduced (catalytically inactive) and its oxidized (catalytically active) form, A(semi) and A(ox), respectively; a protonated intermediate B; the transition state for the rate-determining hydrogen abstraction step C, and its product D. For A and B the electronic properties of the biomimetic compound are qualitatively very similar to the ones of the natural target. However, in agreement with the experimentally observed difference in catalytic activity, the calculated activation energy for the hydrogen abstraction step is distinctly lower for GOase (16 kcal/mol) than for the mimetic compound (21 kcal/mol). The enzymatic transition state is stabilized by a delocalization of the unpaired spin density over the sulfur-modified equatorial tyrosine Tyr272, an effect that for geometric reasons is essentially absent in the biomimetic compound. Further differences between the mimic and its natural target concern the structure of the product of the abstraction step, which is characterized by a weakly coordinated aldehyde complex for the latter and a tightly bound linear complex for the former.

Binding Sites↗

PubMed2000

Harmonic and anharmonic dynamics of Fe-CO and Fe-O(2) in heme models.

We present density-functional molecular dynamics simulations of FeP(Im)(AB) heme models (AB = CO, O(2), Im = imidazole) as a way of sketching the dynamic motion of the axial ligands at room temperature. The FeP(Im)(CO) model is characterized by an essentially upright FeCO unit, undergoing small deviations with respect to its linear equilibrium structure (bending and tilting up to 10 degrees and 7 degrees, often occur). The motion of the carbon monoxide ligand is found to be quite complex and fast, its projection on the porphyrin plane sampling all the porphyrin quadrants in a short time ( approximately 0.5 ps). Simultaneously, the imidazole ligand rotates slowly around the Fe-N(epsilon) bond. In contrast to carbon monoxide, the oxygen ligand in FeP(Im)(O(2)) prefers a conformation where the projection of the O-O axis on the porphyrin plane bisects one of the porphyrin quadrants. A transition to other quadrants takes place through an O-O/Fe-N(p) overlapping conformation, within 4-6 ps. Further details of these mechanisms and their implications are discussed.

Carbon Monoxide↗

PubMed1999

Superionic and metallic states of water and ammonia at giant planet conditions.

The phase diagrams of water and ammonia were determined by constant pressure ab initio molecular dynamic simulations at pressures (30 to 300 gigapascal) and temperatures (300 to 7000 kelvin) of relevance for the middle ice layers of the giant planets Neptune and Uranus. Along the planetary isentrope water and ammonia behave as fully dissociated ionic, electronically insulating fluid phases, which turn metallic at temperatures exceeding 7000 kelvin for water and 5500 kelvin for ammonia. At lower temperatures, the phase diagrams of water and ammonia exhibit a superionic solid phase between the solid and the ionic liquid. These simulations improve our understanding of the properties of the middle ice layers of Neptune and Uranus.

Ammonia↗

PubMed1997

On the Quantum Nature of the Shared Proton in Hydrogen Bonds

The relative influence of thermal and quantum fluctuations on the proton transfer properties of the charged water complexes H5O2+ and H3O2- was investigated with the use of ab initio techniques. These small systems can be considered as prototypical representatives of strong and intermediate-strength hydrogen bonds. The shared proton in the strongly hydrogen bonded H5O2+ behaved in an essentially classical manner, whereas in the H3O2- low-barrier hydrogen bond, quantum zero-point motion played a crucial role even at room temperature. This behavior can be traced back to a small difference in the oxygen-oxygen separation and hence to the strength of the hydrogen bond.

Journal Article↗

PubMed1996