Truncation studies

In the case of two chemokines with G-terminal tails (e.g., lymphotactin/ XGLl and M1G/GXGL9), truncation studies have shown that these domains are also critical for function (Glark-Lewis et al, 2003 Hedrick et al, 1997). Interestingly, like the N-terminal triggering domain, in XGLl, the G-terminal tail is unstructured. 

By contrast, peptide 124 was found to populate a canonical type 11 p-tum in its lowest energy ensemble (Fig. 13b). That it was discovered from a random combinatorial library speaks to the possibly privileged nature of this secondary structure element [188]. Furthermore [183], the structure validated a number of hypotheses based on sequence variations and truncation studies that support a remote hydroxyl-directed mechanism of action for the oxidation of the 6,7-position of famesol by 124. Importantly, a sidechain ether is implicated as a key acceptor of a hydrogen bond from famesol. 

All static studies at pressures beyond 25 GPa are done with diamond-anvil cells conceived independently by Jamieson [32] and by Weir etal [33]. In these variants of Bridgman s design, the anvils are single-crystal gem-quality diamonds, the hardest known material, truncated with small flat faces (culets) usually less than 0.5 nun in diameter. Diamond anvils with 50 pm diameter or smaller culets can generate pressures to about 500 GPa, the highest static laboratory pressures equivalent to the pressure at the centre of the Earth. 

In applying minimal END to processes such as these, one finds that different initial conditions lead to different product channels. In Figure 1, we show a somewhat truncated time lapse picture of a typical trajectory that leads to abstraction. In this rendering, one of the hydrogens of NHaD" " is hidden. As an example of properties whose evolution can be depicted we display interatomic distances and atomic electronic charges. Obviously, one can similarly study the time dependence of various other properties during the reactive encounter. 

For large systems comprising 36,000 atoms FAMUSAMM performs four times faster than SAMM and as fast as a cut-off scheme with a 10 A cut-off distance while completely avoiding truncation artifacts. Here, the speed-up with respect to SAMM is essentially achieved by the multiple-time-step extrapolation of local Taylor expansions in the outer distance classes. For this system FAMUSAMM executes by a factor of 60 faster than explicit evaluation of the Coulomb sum. The subsequent Section describes, as a sample application of FAMUSAMM, the study of a ligand-receptor unbinding process. 

In periodic boimdary conditions, one possible way to avoid truncation of electrostatic interaction is to apply the so-called Particle Mesh Ewald (PME) method, which follows the Ewald summation method of calculating the electrostatic energy for a number of charges [27]. It was first devised by Ewald in 1921 to study the energetics of ionic crystals [28]. PME has been widely used for highly polar or charged systems. York and Darden applied the PME method already in 1994 to simulate a crystal of the bovine pancreatic trypsin inhibitor (BPTI) by molecular dynamics [29]. 

The use of QM-MD as opposed to QM-MM minimization techniques is computationally intensive and thus precluded the use of an ab initio or density functional method for the quantum region. This study was performed with an AMi Hamiltonian, and the first step of the dephosphorylation reaction was studied (see Fig. 4). Because of the important role that phosphorus has in biological systems [62], phosphatase reactions have been studied extensively [63]. From experimental data it is believed that Cys-i2 and Asp-i29 residues are involved in the first step of the dephosphorylation reaction of BPTP [64,65]. Alaliambra et al. [30] included the side chains of the phosphorylated tyrosine, Cys-i2, and Asp-i 29 in the quantum region, with link atoms used at the quantum/classical boundaries. In this study the protein was not truncated and was surrounded with a 24 A radius sphere of water molecules. Stochastic boundary methods were applied [66]. 

One of the more important uses of OM is the study of crystallization growth rates. K. Cermak constructed an interference microscope with which measurements can be taken to 50° (Ref 31). This app allows for study of the decompn of the solution concentrated in close proximity to the growing crystal of material such as Amm nitrate or K chlorate. In connection with this technique, Stein and Powers (Ref 30) derived equations for growth rate data which allow for correct prediction of the effects of surface nucleation, surface truncation in thin films, and truncation by neighboring spherulites... 

Experimentation showed that the protein was not glycosylated and that the sequence at the iV-amino acid terminus corresponded to that expected. The C-terminus sequence, however, did not correspond to that predicted and these data were interpreted in terms of the presence of a heterogeneous, truncated, protein. A study of the tryptic digest fragments from this protein with matrix-assisted laser desorption ionization (MALDI) with post-source decay enabled the authors to suggest the positions at which the parent protein had been truncated. 

These treatments of periodic parts of the dipole moment operator are supported by several studies which show that, for large oligomeric chains, the perturbed electronic density exhibits a periodic potential in the middle of the chain whereas the chain end effects are related to the charge transfer through the chain [20-21]. Obviously, approaches based on truncated dipole moment operators still need to demonstrate that the global polarization effects are accounted for. In other words, one has to ensure that the polymeric value corresponds to the asymptotic limit of the oligomeric results obtained with the full operator. 

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