Development of the force field parameters for phosphoimidazole and phosphohistidine

Phosphorylation of histidine-containing proteins is a key step in the mechanism of many phosphate transfer enzymes (kinases, phosphatases) and is the first stage in a wide variety of signal transduction cascades in bacteria, yeast, higher plants, and mammals. Studies of structural and dynamical aspects of such enzymes in the phosphorylated intermediate states are important for understanding the intimate molecular mechanisms of their functioning. Such information may be obtained via molecular dynamics and/or docking simulations, but in this case appropriate force field parameters for phosphohistidine should be explicitly defined. In the present article we describe development of the GROMOS96 force field parameters for phosphoimidazole molecule--a realistic model of the phosphohistidine side chain. The parameterization is based on the results of ab initio quantum chemical calculations with subsequent refinement and testing using molecular mechanics and molecular dynamics simulations. The set of force constants and equilibrium geometry is employed to derive force field for the phosphohistidine moiety. Resulting parameters and topology are incorporated into the molecular modeling package GROMACS and used in molecular dynamics simulations of a phosphohistidine-containing protein in explicit solvent.     

Characterization and comparison of metal accumulation in two Escherichia coli strains expressing either CopA or MntA, heavy metal-transporting bacterial P-type adenosine triphosphatases

MntA from Lactobacillus plantarum and copA from Enterococcus hirae both encode membrane proteins that are members of the P-type family of adenosine triphosphatases (ATPases). Both transporters act as metal importers to take up nutritionally required substrates; MntA translocates Mn(II) and CopA translocates Cu(I). Both ATPases can also translocate secondary substrates, Cd(II) and Ag(I), respectively. Although functionally and sequentially similar, these ATPases differ in several key residues and in their membrane topologies. The bioaccumulation properties of these two proteins were examined by coexpressing the transporters with overexpressed metallothionein in Escherichia coli cells, a system that has previously shown high levels of substrate-specific uptake. Both strains exhibited rapid metal accumulation, both saturated at around 50 μM metal, and both displayed temperature-sensitive uptake. However, the transporters responded differently when external conditions were varied; MntA displayed increased sensitivity to ionic strength, while CopA was more pH sensitive and more inhibited by chelating agents. The differences in accumulation are likely owing to structural differences in the transmembrane region of these two ATPases.     

Sequential exoproteolysis as a structural probe: a cautionary note

In a recent paper, Villaneuva et al. (J. Mass Spectrom. 2002; 37: 974) described the use of exoproteases as probes of higher order structure in proteins. Their model assumes that the proteins are attacked sequentially from either the N-terminus or the C-terminus, depending on the type of exoprotease (aminopeptidase or carboxypeptidase) used. The products of this presumed exoproteolysis were then analysed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The pattern of fragments obtained was mapped on to the primary sequence of the protein, and the exoproteolysis was interpreted as comprising a series of fast and slow phases, the rates of the different phases being directly related to the higher order structure of particular segments of the protein. Here, it is shown that this explanation is unlikely, that both kinetic and practical considerations suggest that alternative explanations for the data should be sought, and that exoproteolysis will perhaps not be as valuable as a conformational probe as the authors suggest.     

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.