On the role of the conserved aspartate in the hydrolysis of the phosphocysteine intermediate of the low molecular weight tyrosine phosphatase

The usual rate-determining step in the catalytic mechanism of the low molecular weight tyrosine phosphatases involves the hydrolysis of a phosphocysteine intermediate. To explain this hydrolysis, general base-catalyzed attack of water by the anion of a conserved aspartic acid has sometimes been invoked. However, experimental measurements of solvent deuterium kinetic isotope effects for this enzyme do not reveal a rate-limiting proton transfer accompanying dephosphorylation. Moreover, base activation of water is difficult to reconcile with the known gas-phase proton affinities and solution phase pK(a)'s of aspartic acid and water. Alternatively, hydrolysis could proceed by a direct nucleophilic attack by a water molecule. To understand the hydrolysis mechanism, we have used high-level density functional methods of quantum chemistry combined with continuum electrostatics models of the protein and the solvent. Our calculations do not support a catalytic activation of water by the aspartate. Instead, they indicate that the water oxygen directly attacks the phosphorus, with the aspartate residue acting as a H-bond acceptor. In the transition state, the water protons are still bound to the oxygen. Beyond the transition state, the barrier to proton transfer to the base is greatly diminished; the aspartate can abstract a proton only after the transition state, a result consistent with experimental solvent isotope effects for this enzyme and with established precedents for phosphomonoester hydrolysis.     

Cumulant functions in optical coherence theory

Cumulant functions are introduced to describe the statistical state of a radiation field. These functions are simply related to the optical coherence functions but have some interesting features. It is shown that if the cumulant functions of all orders greater than some numberN ₀ vanish then they also vanish for all orders greater than 2. Thermal field is the only field having this property. This property holds whether the field is described by a classical stochastic process or by a quantum density operator. Further the particular operator ordering used in defining these cumulant functions for the quantized field affects only the second order cumulant function. To describe the statistical state of a vector field such as partially polarized or unpolarized radiation, one would need to introduce cumulant tensors.     

Evoking biphone neighborhoods with verbal transformations: illusory changes demonstrate both lexical competition and inhibition

When a recorded verbal stimulus repeats over and over, perceptual changes occur and listeners hear competing forms. These verbal transformations (VTs) were obtained for a phonemically related set of 24 consonant-vowel syllables that varied widely in frequency-weighted neighborhood density (FWND). Listener's initial transformations involving substitution of consonants versus vowels were strongly correlated with the lexical substitution neighborhood [r=+0.82, p<0.0001]. Interestingly, as stimulus FWND increased, average time spent hearing illusory forms substantially decreased [r=-0.75, p<0.0001]. These results suggest that VTs not only reveal underlying competitors, but also provide a highly sensitive measure of lexical inhibition.     

Gas phase activation energy for unimolecular dissociation of biomolecular ions determined by focused RAdiation for gaseous multiphoton ENergy transfer (FRAGMENT)

We present a novel approach for the determination of activation energy for the unimolecular dissociation of a large (>50 atoms) ion, based on measurement of the unimolecular dissociation rate constant as a function of continuous-wave CO(2) laser intensity. Following a short ( approximately 1 s) induction period, CO(2) laser irradiation produces an essentially blackbody internal energy distribution, whose 'temperature' varies inversely with laser intensity. The only currently available method for measuring such activation energies is blackbody infrared radiative dissociation (BIRD). Compared with BIRD, FRAGMENT: (a) eliminates the need to heat the surrounding ion trap and vacuum chamber to each of several temperatures (each requiring hours for temperature equilibration); (b) offers a three-fold wider range of effective blackbody temperature; and (c) extends the range of applications to include initially cold ions (e.g., gas-phase H/D exchange). Our FRAGMENT-determined activation energy for dissociation of protonated bradykinin, 1.2 +/- 0.1 eV, agrees within experimental error to the value, 1.3 +/- 0.1 eV, previously reported by Williams et al. from BIRD experiments. Copyright 1999 John Wiley & Sons, Ltd.     

Multiple-site ligand binding to flexible macromolecules: Separation of global and local conformational change and an iterative mobile clustering approach

This article concerns the calculation of equilibria of ligand binding to multiple sites in macromolecules in the presence of conformational flexibility and conformation-dependent interaction among the sites. A formulation of this problem is presented in which global conformational changes are distinguished from conformational changes that are confined to “locally flexible regions.” The formalism is quite general in that ligands of different types, multivalent binding sites, tautomeric binding sites, and sites that bind more than one type of ligand can be accommodated. Strictly speaking, the separation of the conformational problem into global and local parts does not impose any loss of generality, although in practice it is necessary to restrict the number of global and local conformers. Because of the combinatorics of binding and conformational states, the computational complexity of a problem having only local conformational flexibility grows exponentially with the number of sites and the number of locally flexible regions. An iterative mobile clustering method for cutting off this exponential growth and obtaining approximate solutions with low computational cost is presented and tested. In this method, a binding site is selected, and a “cluster” of strongly interacting sites is set up around it; within the cluster, the binding and conformational states are fully enumerated, whereas the influences of sites outside the cluster on the sites inside are treated by a mean field approximation. The procedure then moves to the next site around which another (possibly overlapping) cluster is formed and the calculation is repeated. The procedure iterates through the list of sites in this way, using the results of previous iterations for the mean-field terms of current iterations until a convergence criterion is met. The method is tested on a large set of randomly generated problems of varying size, whose geometries are chosen to have protein-like statistical properties. It is found that the method is accurate and rapid with the computational cost scaling linearly to quadratically with the number of sites, except for a minority of cases in which large clusters occur by chance. The new method is more accurate than a Monte Carlo method, and may be faster or slower depending on the clustering criteria and details of the macromolecule. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1091–1111, 1999     

Model for proton transport coupled to protein conformational change: application to proton pumping in the bacteriorhodopsin photocycle

A modeling method is presented for protein systems in which proton transport is coupled to conformational change, as in proton pumps and in motors driven by the proton-motive force. Previously developed methods for calculating pKa values in proteins using a macroscopic dielectric model are extended beyond the equilibrium case to a master-equation model for the time evolution of the system through states defined by ionization microstate and a discrete set of conformers. The macroscopic dielectric model supplies free energy changes for changes of protonation microstate, while the method for obtaining the energetics of conformational change and the relaxation rates, the other ingredients needed for the master equation, are system dependent. The method is applied to the photoactivated proton pump, bacteriorhodopsin, using conformational free energy differences from experiment and treating relaxation rates through three adjustable parameters. The model is found to pump protons with an efficiency relatively insensitive to parameter choice over a wide range of parameter values, and most of the main features of the known photocycle from very early M to the return to the resting state are reproduced. The boundaries of these parameter ranges are such that short-range proton transfers are faster than longer-range ones, which in turn are faster than conformational changes. No relaxation rates depend on conformation. The results suggest that an "accessibility switch", while not ruled out, is not required and that vectorial proton transport can be achieved through the coupling of the energetics of ionization and conformational states.     

Enhancing intelligibility of narrowband speech with out-of-band noise: evidence for lateral suppression at high-normal intensity

Previous studies have shown that the intelligibility of filtered speech can be enhanced by filling stopbands with noise. The present study found that this enhancement occurred only when speech intensity was sufficiently high to degrade performance. Intelligibility decreased by about 15% when narrowband speech was increased from 45 to 65 dBA (corresponding to broadband speech levels of about 60 and 80 dBA), and decreased by 20% at a level of 75 dBA. However, when flanking bands of low-pass and high-pass filtered white noise were added at spectrum levels of -40 to -20 dB relative to the speech, intelligibility of the 75-dBA speech band increased by about 13%. Additional findings confirm that this enhancement of intelligibility depends upon out-of-band stimulation, in agreement with theories proposing that lateral suppressive interactions extend the dynamic range of intensity coding by counteracting effects of auditory-nerve firing-rate saturation at high signal levels.