Specificity canonical site

Although some noncanonical EcoRI sites are methylated in vitro with only fivefold lower specificities than the canonical site, the noncanonical sites (e.g., TAATTC, CAATTC, GTATTC, and GGATTC) remain unmethylated in vivo in the presence of M EcoRI (28). The high in vivo specificity of M EcoRI is partly attributed to the active removal of methylated sequences by DNA repair enzymes. 

As mentioned in Sect. I, even the simplest electrosorption systems are extremely complicated. This complexity means that a comprehensive theoretical description that enables predictions for phenomena on macroscopic scales of time and space is still generally impossible with present-day methods and technology. (Note that MD simulations, such as those presented in Sect. II, are only possible up to times of a few himdred nanoseconds.) Therefore, it is necessary to use a variety of analytical and computational methods and to study various simplified models of the solid-hquid interface. One such class of simpHfied models are LG models, in which chemisorbed particles (solutes or solvents) can only be located at specific adsorption sites, commensurate with the substrate s crystal structure. This can often be a very good approximation, for instance, for halides on the (100) surface of Ag, for which it can be shown that the adsorbates spend the vast majority of their time near the fourfold hollow surface sites. A LG approximation to such a continuum model, appropriate for chemisorption of small molecules or ions, ° is defined by the discrete, effective grand-canonical Hamiltonian,... 

A MC study of adsorption of living polymers [28] at hard walls has been carried out in a grand canonical ensemble for semiflexible o- 0 polymer chains and adsorbing interaction e < 0 at the walls of a box of size C. A number of thermodynamic quantities, such as internal energy (per lattice site) U, bulk density (f), surface coverage (the fraction of the wall that is directly covered with segments) 9, specific heat C = C /[k T ]) U ) — U) ), bulk isothermal compressibility... 

Enumerate all the microstates of the molecule. Each microstate of the molecule, having k ligands bound to k specific sites, is characterized by an energy level Ej(k). We usually combine many microstates into one macrostate denoted by a, and write the corresponding canonical PF as... 

Sum over all macrostates a of the molecule to obtain the canonical PF of the molecule with k ligands bound to k specific sites (s),... 

In some cases where the canonical PF of all the ( ) specific configurations are equal, we say that the system has m identical sites in the strict sense. Only in this case does the last equality on the rhs of Eq. (1.4.3) hold. Thus, from Eq. (1.4.1) to (1.4.3) we have proceeded from Jik) to Qjik), the latter being the canonical PF of an adsorbent molecule with k (unspecified) sites occupied by ligands. 

In summary, the intrinsic binding constant to be used throughout this book always refers to a specific set of sites. They are defined in terms of the molecular properties of the system through the corresponding canonical PFs. They are also interpreted as probability ratios or as free energies of binding processes. In subsequent chapters we shall see how to extract from these quantities various correlation functions or, equivalently, cooperativities. 

The modified Mth RIRl, Mxe GyrA, and Ssp DnaB mini-inteins have been recently applied to the isolation of proteins with an N-terminal cysteine residues (29,30). These inteins undergo temperature- and pH-dependent C-termi-nal cleavage when the N-terminal cysteine residue of the intein is substituted with alanine (Table 2). The target protein is recombinantly expressed as a fusion protein with the C-terminal intein tag (31) (Fig. 3B). After intein splicing the protein that possesses N-terminal cysteine is generated. Moreover, such a protein can be obtained by total chemical synthesis and different chemical labels or non-canonical amino acids can be site-specifically incorporated into the sequence. 

The aaRSs possess diverse polypeptide domains and insertions, in addition to their catalytic core. Likely, these domains evolved to enhance specificity and fidelity and, in some cases, confer other functions (4, 5). One such domain is the C-terminal anticodon-binding domain that is widely varied (1). For example, GluRS and GlnRS have highly conserved active sites within their canonical aminoacylation cores but have appended N-terminal anticodon-binding domains that are composed primarily of either a-helices or fS-strands, respectively. In addition, common RNA-binding protein domains such as the OB-fold have been incorporated into aaRSs such as LysRS-II. In at least half of the aaRSs, an internal or appended domain confers amino acid editing activity (3). 

The most thoroughly studied mechanism of protein protease inhibitors is that of the standard mechanism (or Canonical or Laskowski mechanism) inhibitors of serine proteases (1) (Fig. 2). Standard mechanism inhibitors include the Kazal, Kunitz, and Bowman-Birk family of inhibitors and bind in a lock-and-key fashion. Ah standard mechanism inhibitors insert a reactive loop into the active site of the protease, which is complementary to the substrate specificity of the target protease and binds in an extended fi-sheet with the enzyme in a substrate-like manner. WhUe bound to the protease, the scissile bond of standard mechaiusm inhibitors is hydrolyzed very slowly, but products are not released and the amide bond is re-ligated. The standard mechanism is an efficient way to inhibit serine proteases, and it is thus used by many structurally... 

Two-dimensional representations alternative to the molecular graph are the linear notation systems, for example, Wiswesser Line Notation system (WLN) [Smith and Baker, 1975], SMILES [Weininger, 1988, 1990, 2003 Weininger, Weininger et al., 1989 Convard, Dubost et al., 1994 Hinze and Welz, 1996], and SMARTS (SMART - Daylight Chemical Information Systems, 2004). CAST (CAnonical representation of STereochemistry) is a method that gives a linear notation that canonically represents stereochemistry around a specific site in a molecule [Satoh, Koshino et al, 2000, 2001, 2002],... 

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