Probing the Conformational Stability of Two Different Copper Proteins: A Dynamic Fluorescence Study on Azurin and Ascorbate Oxidase

Tryptophan fluorescence is extremely useful to monitor structural conformational transitions in proteins. Denaturant-induced unfolding of azurin and ascorbate oxidase has been studied by dynamic fluorescence measurements in the frequency domain and the results have been interpreted in terms of continuous distribution of lifetimes. The data add new information on the unfolding mechanism that was previously analyzed by steady-state emission spectroscopy. In particular, the existence of multiple, parallel unfolding pathways may be envisaged and correlated, in both cases, to the two protein structures. The effect of metal depletion has been also characterized by fluorescence lifetime measurements. In the case of azurin, a monomeric protein, the data demonstrate that copper removal yields a totally different unfolding pathways with respect to the holo protein, indicating that metal ion plays a fundamental structural role in the wild type, native protein. In the case of ascorbate oxidase a dimer of 140 kDa, only minor effects have been detected by copper removal. However, the analysis of the fluorescence decay in presence of different amounts of guanidinium hydrochloride gives new important insights on the unfolding intermediates. In particular the data support the hypothesis of a partial exposure of an outer layer of dimer at intermediate denaturant concentration. This ability of dynamic fluorescence to pinpoint the presence of structural micro-heterogeneity in the unfolding pathways of proteins demonstrates the greater power of this technique compared to the most commonly used steady-state measurements.     

Solvent viscosity dependence of the folding rate of a small protein: distributed computing study

By using distributed computing techniques and a supercluster of more than 20,000 processors we simulated folding of a 20-residue Trp Cage miniprotein in atomistic detail with implicit GB/SA solvent at a variety of solvent viscosities (gamma). This allowed us to analyze the dependence of folding rates on viscosity. In particular, we focused on the low-viscosity regime (values below the viscosity of water). In accordance with Kramers' theory, we observe approximately linear dependence of the folding rate on 1/gamma for values from 1-10(-1)x that of water viscosity. However, for the regime between 10(-4)-10(-1)x that of water viscosity we observe power-law dependence of the form k approximately gamma(-1/5). These results suggest that estimating folding rates from molecular simulations run at low viscosity under the assumption of linear dependence of rate on inverse viscosity may lead to erroneous results.     

Gas-phase activation and reaction dynamics of chiral ion-dipole complexes

A family of enantiomerically pure oxonium ions, that is O-protonated 1-aryl-1-methoxyethanes, has been generated in the gas phase by the (CH(3))(2)Cl(+) methylation of the corresponding 1-arylethanols. Some information on their reaction dynamics was obtained from a detailed kinetic study of their inversion of configuration and dissociation. The activation parameters of the inversion reaction are found to obey two different isokinetic relationships depending upon the nature and the position of the substituents in the oxonium ions. In contrast, the activation parameters of the dissociation reaction obey a single isokinetic relationship. The inversion and dissociation rate constants do not follow simple linear free-energy relationships. This complicated kinetic picture has been rationalized in terms of different activation dynamics in gaseous CH(3)Cl, which, in turn, determine the reaction dynamics of the oxonium ion. When the predominant activation of the oxonium ion involves resonant energy exchange from the 1015 cm(-1) CH(3) rocking mode of unperturbed CH(3)Cl, the inversion reaction proceeds through the dynamically most favored TS, characterized by the unassisted C(alpha)bond;O bond elongation. When, instead, the activation of the oxonium ions requires the formation of an intimate encounter complex with CH(3)Cl, the inversion reaction takes place via the energetically most favored TS, characterized by multiple coordination of the CH(3)OH moiety with the H(alpha) and H(ortho) atoms of the benzylic residue. The activation dynamics operating in the intimate encounter complex with CH(3)Cl is also responsible for the dissociation of most selected oxonium ions.     

Jerk Influence Coefficients,via Screw Theory,of Closed Chains

In this paper a novel method for determining the kinematic influence coefficients up to the jerk analysis of closed chains with multiple degrees of freedom by means of screw theory, also known as motor algebra, is introduced. A closed chain is obtained by rigidly attaching the end-effector of a serial chain to the base link. This condition ensures that the velocity, acceleration, and jerk, both angular and of any point fixed to the end-effector are zero. Afterwards, a comparison between the kinematic equations of motion, up to the jerk analysis, obtained by traditional methods with those obtained by means of screw theory reveals the corresponding influence coefficients associated to the generalized coordinates employed to represent the motion of the closed chain. Finally, a numerical example is provided. Sommario. In questo lavoro viene proposto un nuovo metodo per la determinazione dei coefficienti che consentono di sviluppare l'analisi cinematica (jerk incluso) di catene chiuse a molti gradi di liberta' per mezzo della screw theory o algebra dei moti spaziali. La catena chiusa e' ottenuta attaccando rigidamente l'end-effector di una catena seriale al membro di base. Questa condizione assicura che velocita' accelerazione e jerk, sia nel moto angolare che per ciascun punto solidale con l'end-effector siano nulli. Un confronto tra le equazioni cinematiche del moto, inclusa l'analisi del jerk, ottenute con metodi tradizionali e quelle ottenute dalla screw theory, mostra i corrispondenti coefficienti di influenza associati alle coordinate generalizzate impiegate per descrivere il moto della catena chiusa. Un esempio numerico conclude il lavoro.     

Electronic structure of three-dimensional quantum dots

We study the electronic structure of three-dimensional quantum dots using the Hartree-Fock approximation. The confining potential of the electrons in the quantum dot is assumed to be spatially isotropic and harmonic. For up to 40 interacting electrons the ground-state energies and ground-state wavefunctions are calculated at various interaction strengths. The quadrupole moments and electron densities in the quantum dot are computed. Hund's rule is confirmed and a shell structure is identified via the addition energies and the quadrupole moments. While most of the shell structure can be understood on the basis of the unperturbed non-interacting problem, the interplay of an avoided crossing and the Coulomb interaction results in an unexpected closed shell for 19 electrons. Received 5 November 2001 / Received in final form 12 November 2002 Published online 1st April 2003 RID="a" ID="a"e-mail: vorrath@physnet.uni-hamburg.de     

Scaling behavior of a nonlinear oscillator with additive noise,white and colored

We study analytically and numerically the problem of a nonlinear mechanical oscillator with additive noise in the absence of damping. We show that the amplitude, the velocity and the energy of the oscillator grow algebraically with time. For Gaussian white noise, an analytical expression for the probability distribution function of the energy is obtained in the long-time limit. In the case of colored, Ornstein-Uhlenbeck noise, a self-consistent calculation leads to (different) anomalous diffusion exponents. Dimensional analysis yields the qualitative behavior of the prefactors (generalized diffusion constants) as a function of the correlation time. Received 10 October 2002 Published online 6 March 2003 RID="a" ID="a"e-mail: mallick@spht.saclay.cea.fr