Alanine model

These estimates concur with simulation observations for a more complex nonlinear system, a blocked alanine model [67]. Specifically, Verlet becomes... 

Pig. 9. Mean total energy vs. At for the Verlet (a = 0), IM (a = 1/4) and LIM2 (fv = 1/2) schemes for the blocked alanine model. The three lines correspond to averaging energies over an increasing number of steps 2 x 10 (dotted line), 6 x 10 (dashed line), and 10 (solid line). 

Fig. 10. Differences in potential energy components for the blocked alanine model (for bond length, bond angle, dihedral angle, van der Waals, and electrostatic terms, shown top to bottom) before and after the residual corrections in LIN trajectories at timesteps of 2 fs (yellow), 5 fs (red), and 10 fs (blue).

A detailed examination of LN behavior is available [88] for the blocked alanine model, the proteins BPTI and lysozyme, and a large water system, compared to reference Langevin trajectories, in terms of energetic, geometric, and dynamic behavior. The middle timestep in LN can be considered an adjustable quantity (when force splitting is used), whose value does not significantly affect performance but does affect accuracy with respect to the reference trajectories. For example, we have used Atm = 3 fs for the proteins in vacuum, but 1 fs for the water system, where librational motions are rapid. 

The MaxEnt valence density for L-alanine has been calculated targeting the model structure factor phases as well as the amplitudes (the space group of the structure is acentric, Phlih). The core density has been kept fixed to a superposition of atomic core densities for those runs which used a NUP distribution m(x), the latter was computed from a superposition of atomic valence-shell monopoles. Both core and valence monopole functions are those of Clementi [47], localised by Stewart [48] a discussion of the core/valence partitioning of the density, and details about this kind of calculation, may be found elsewhere [49], The dynamic range of the L-alanine model... 

Gaussian noise has been added onto the structure factor amplitudes squared as computed from the L-alanine model density for each datum, the amount of noise added was proportional to the experimental esd for the corresponding intensity measurement ... 

Plate 11 Poly alanine model of ALBP built into electron-density map. This section of the final ALBP model is shown in Plate 2. (For discussion, see Chapter 7.)... 

V. A. Yaylayan and L. J. W. Haffenden, Mechanism of imidazole and oxazole formation in [13C-2]-labelled glycine and alanine model systems, Food Chem., 2003, 81, 403 109. 

Cabezas C, Varela M, Cortijo V, Jimenez AI, Pena I, Daly AM, Lopez JC, Cativiela C, Alonso JL (2013) The alanine model dipeptide Ac-Ala-NH2 exists as a mixture of and C5 conformers. Phys Chem Chem Phys 15 2580... 

Panel 1.1 The 20 different amino acids that occur in proteins. Only side chains are shown, except for the first amino acid, alanine, where all atoms are shown. The bond from the side chain to Ca is red. A ball-and stick model, the chemical formula, the full name, and the three-letter and one-letter codes are given for each amino acid. 

Figure 14.2 Models of a collagen-like peptide with a mutation Gly to Ala in the middle of the peptide (orange). Each polypeptide chain is folded into a polyproline type II helix and three chains form a superhelix similar to part of the collagen molecule. The alanine side chain is accommodated inside the superhelix causing a slight change in the twist of the individual chains, (a) Space-filling model, (b) Ribbon diagram. Compare with Figure 14.1c for the change caused by the alanine substitution. (Adapted from J. Bella et al.. Science 266 75-81, 1994.)...

Molar absorptivity. 502 Molecular ion (M+), 410 Molecular mechanics. 130 Molecular model, dopamine, 930 acetaminophen, 29 acetylene, 18 adenine, 67 adrenaline, 323 alanine, 28, 1016 alanylserine, 1028 rr helix, 1039 p-aminobenzoic acid, 25 anti periplanar geometry, 387 a recoline, 79 aspartame, 29 aspirin. 17 ball-and-stick, 61 /3-pleated sheet, 1039 p-bromoacetophenone, 449 bromocyclohexane, 121 butane, 80... 

The classical cadherins are translated as precursor because they are N-terminally cleaved to reveal the mature proteins. This processing is required to activate the cell adhesion function of cadherins. Cadherins interact in trans (i.e., from opposite cells) via the most N-terminal cadherin rqDeats. A short amino acid sequence within this repeat, histidine-alanine-valine (HAV), has been implicated in mediating cell-cell contacts as HAV peptides can disrupt cadherin-dependent cell adhesion. Besides the trans-interactions of cadherins, the extracellular domains are also capable of forming cis-dimers through lateral amino acid contacts between cadherin molecules on one cell. This dimerization again mainly involves the first cadherin repeat. A zipper model based on the pattern of alternating cis- and trans-dimers [1] for the adhesive interactions has been proposed. 

Fig. 3.15 Model for allosteric inhibition of a protein-DNA complex by a polyamide-inter-calator conjugate. (Top) The GCN4 homodimer (yellow) is displaced by the intercalating moiety (green) of the polyamide conjugate. Blue and red spheres represent pyrrole and imidazole amino acids, respectively. The blue diamond represents / -alanine. (Bottom, left) Hydrogen-bonding model of an eight-ring hairpin polyamide-intercalator conjugate...

This model clearly shows that the catalytic machinery involves a dyad of histidine and aspartate together with the oxyanion hole. Hence, it does not involve serine, which is the key amino acid in the hydrolytic activity of lipases, and, together with aspartate and histidine, constitutes the active site catalytic triad. This has been confirmed by constructing a mutant in which serine was replaced with alanine (Serl05Ala), and finding that it catalyzes the Michael additions even more efficiently than the wild-type enzyme (an example of induced catalytic promiscuity ) [105]. 

The three-point pharmacophore models are shown in Fig. 7. The structures of the y0-alanine analogues and their antiepileptic activities against pilocarpine test are tabulated in Table 3. 

---