Coordination numbers amino acids

Fig. 1 Blocks of multiple sequence alignment of protein sequences of carboxypeptidases from B. taurus, Mus musculus, Rattus norvegicus, Neurospora crassa, Schizosaccharomyces pombe, Drosophila melanogaster, and Homo sapiens along with protein sequence from H. pylori (Uniprot accession code HPAG1 0372 from strain HPAG1). Numbers on the top correspond to amino acid residue number of the carboxypeptidase enzyme from B. taurus. Gray vertical columns indicate conserved residues. Amino acid residues corresponding to Glu-182 and His-306, which coordinate to zinc, are conserved, whereas another Zn-coordinating amino acid residue corresponding to His-179 is substituted by Gin in the Helicobacter sequence. Functionally important residues corresponding to Arg-237 are also conserved...

Fig. 15.5. Transformation of force-extension traces into the molecular coordinate contour length, (a) The rupture force and the extension xi and X2 are subject to fluctuations and exhibit a broad distribution. Furthermore, they depend on experimental parameters as described in the text. The characteristic parameter of a folding state is the free contour length as illustrated in (b). Each data point (Fi, Xi) is transformed into force-contour length space (Fi, Li) by means of inverse models for polymer elasticity. The transformed data points are accumulated into histograms, which directly show the barrier positions Li and L2 along the contour length, (c) The barrier positions of TK in the absence (black) and presence (red) of ATP were determined with a relative error of 2% corresponding to only a few amino acids. The number of amino acids (346 6) agrees well with the actual number (344). (b) Ig/Fn domains serve as an internal verification. The determined mean number of 95 2 amino acids agrees again with the value of 96 aa...

Of particular interest in biology are the coordination compounds formed between metal ions and ligand groups on amino acids. A number of enzymes are active only when they have formed a complex with a metal ion. The best understood metallo-enzyme is carboxypeptidase this occurs in the digestive system, and its structure has been determined by X-ray diffraction p. 107). The usual form of the enzyme contains... 

There are a few documented examples of studies of ligand effects on hydrolysis reactions. Angelici et al." investigated the effect of a number of multidentate ligands on the copper(II) ion-catalysed hydrolysis of coordinated amino acid esters. The equilibrium constant for binding of the ester and the rate constant for the hydrolysis of the resulting complex both decrease in the presence of ligands. Similar conclusions have been reached by Hay and Morris, who studied the effect of ethylenediamine... 

Also the arene-arene interactions, as encountered in Chapter 3, are partly due to hydrophobic effects, which can be ranked among enforced hydrophobic interactions. Simultaneous coordination of an aromatic oc amino acid ligand and the dienophile to the central copper(II) ion offers the possibility of a reduction of the number of water molecules involved in hydrophobic hydration, leading to a strengthening of the arene-arene interaction. Hence, hydrophobic effects can have a beneficial influence on the enantioselectivity of organic reactions. This effect is anticipated to extend well beyond the Diels-Alder reaction. 

A prior distribution for sequence profiles can be derived from mixtures of Dirichlet distributions [16,51-54]. The idea is simple Each position in a multiple alignment represents one of a limited number of possible distributions that reflect the important physical forces that determine protein structure and function. In certain core positions, we expect to get a distribution restricted to Val, He, Met, and Leu. Other core positions may include these amino acids plus the large hydrophobic aromatic amino acids Phe and Trp. There will also be positions that are completely conserved, including catalytic residues (often Lys, GIu, Asp, Arg, Ser, and other polar amino acids) and Gly and Pro residues that are important in achieving certain backbone conformations in coil regions. Cys residues that form disulfide bonds or coordinate metal ions are also usually well conserved. 

The extracellular domain of cadherins consists of a variable number of a repeated sequence of about 110 amino acids. This sequence is termed the cadherin repeat and resembles in overall structure, but not in sequence, the Ig like domains. The cadherin repeat is the characteristic motive common to all members of the cadherin superfamily. Classical and desmosomal cadherins contain five cadherin repeats, but as many as 34 repeats have been found in the FAT cadherin (see below). Cadherins are calcium-dependent cell adhesion molecules, which means that removal of Ca2+, e.g., by chelating agents such as EDTA, leads to loss of cadherin function. The Ca2+-binding pockets are made up of amino acids from two consecutive cadherin repeats, which form a characteristic tertiary structure to coordinate a single Ca2+ion [1]. 

Figure 18.4 Structures of heme/Cu oxidases at different levels of detail, (a) Position of the redox-active cofactors relative to the membrane of CcO (left, only two obligatory subunits are shown) and quinol oxidase (right), (b) Electron transfer paths in mammalian CcO. Note that the imidazoles that ligate six-coordinate heme a and the five-coordinate heme are linked by a single amino acid, which can serve as a wire for electron transfer from ferroheme a to ferriheme as. (c) The O2 reduction site of mammalian CcO the numbering of the residues corresponds to that in the crystal structure of bovine heart CcO. The subscript 3 in heme as and heme 03 signifies the heme that binds O2. The structures were generated using coordinates deposited in the Protein Data Bank, lari [Ostermeier et al., 1997] Ifft [Abramson et al., 2000] (a) and locc [Tsukihara et al., 1996] (b, c).

The versatile binding modes of the Cu2+ ion with coordination number from four to six due to Jahn-Teller distortion is one of the important reasons for the diverse structures of the Cu-Ln amino acid complexes. In contrast, other transition metal ions prefer the octahedral mode. For the divalent ions Co2+, Ni2+, and Zn2+, only two distinct structures were observed one is a heptanuclear octahedral [LnM6] cluster compound, and the other is also heptanuclear but with a trigonal-prismatic structure. 

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