Serine, molecular structure

Now, it is seen that polar groups dominate the molecular structure, resulting from hydroxyl groups from the two serine and threonine fragments in addition to the peptide bonds themselves. Only weak dispersive interactions will be contributed by glycine fragments (CH2 groups). 

P-Lactamases are enzymes that hydrolyze the P-lactam ring of P-lactamantibiotics (penicillins, cephalosporins, monobactams and carbapenems). They are the most common cause of P-lactam resistance. Most enzymes use a serine residue in the active site that attacks the P-lactam-amid carbonyl group. The covalently formed acylester is then hydrolyzed to reactivate the P-lacta-mase and liberates the inactivated antibiotic. Metallo P-lactamases use Zn(II) bound water for hydrolysis of the P-lactam bond. P-Lactamases constitute a heterogeneous group of enzymes with differences in molecular structures, in substrate preferences and in the genetic localizations of the encoding gene (Table 1). 

Van Alsenoy, C., J. N. Scarsdale, H. L. Sellers, and L. Schafer. 1981. Ab Initio Studies of Structural Features Not Easily Amenable to Experiment. The Molecular structures of Two Low-Energy Forms of Unionized Serine. Chem. Phys. Letters 80, 124-126. 

Pilocarpine (30) is one of a series of related alkaloids found in the South American plant genus Pilocarpus, known commonly as Jaborandi leaf, which was used in traditional medicine to induce sweating and urination. The molecular structure of (30) bears similarities to ACh (2) since the positively-charged N-atom and the lactone binding to the serine are about the same distance apart. Chewing the leaf results in typical features... 

HSL cDNA from rat adipocytes was cloned and sequenced (Holm et al., 1988). The predicted protein is 757 amino acids in length and over 82.8 kDa in size. There is no homology with any other protein. The only sequence feature shared by this enzyme with other lipases is the G-X-S-X-G pentapeptide, which occurs within a stretch reasonably consistent with the /3-eSer-a motif. Thus, Ser-423, which is a part of this pentapeptide, is the likely nucleophile. Nothing is known about the other members of a catalytic triad, if indeed it exists in this enzyme. The regulatory serine that undergoes phosphorylation by cAMP-dependent kinase has been identified as Ser-563 (Holm et al., 1988). Nothing more is known about the molecular structure of this important enzyme. 

Fig. 1. Complex lipid forms and fatty acids in mammalian cells, including triglycerides, phosphatides with either choline, ethanolamine, serine or inositol, and shphigomyeUn. Fatty acid building blocks include oleic acid (CIS 1) and DHA (C22 6) in molecular structure form.

All structures were selected from the Ensemble database. In addition to approved therapeutic agents these particularly include a set of lead compounds entered in advanced clinical/preclinical trials (a total of 16,540 compounds). Structures were extracted according to the assigned activity class, where the class indicates a common target-specific group such as GPCRs, kinases and proteases, nuclear receptors, and ion channels as well as more than 150 subclasses (for example, serotonin, tachykinin and dopamine receptors, tyrosine, Abl, Aurora and serine/threonine kinases, cysteine and serine proteases, etc.). Prior to the statistical experiments, the molecular structures should be filtered and normalized in order to fulfill certain criteria (see Subheading 3.5 and 4). 

In a dilute protein solution, the nano length scale or the molecular structure of protein molecules determines the thermodynamic equilibrium between protein-protein and protein-water interactions. The consequent surface and hydrodynamic properties of proteins are resulted from the proportion of hydrophobic, hydrophilic, and charged amino acid residues. For example, caseins could adopt a random coil structure due to their flexible structure as a result of phosphorylated serine residues caseins indeed lack the ordered structures of a-helix, 3-sheet, and 3-turn found in globular proteins. This gives rise to better multifunctionality of caseins over globular proteins. 

Confirmation of the molecular structure of the enzyme-inactivator adduct has been obtained for few modified PLP-dependent enzymes. In the case of the reaction of aspartate transaminase (aspartate aminotransferase) with L-serine 0-sulfate, the surprising result thus obtained by Metzler and co-workers has forced reevaluation of the mechanism of similar inactivators (Ueno et al., 1982). Conventional wisdom argued that the reaction should involve elimination of sulfate from the inactivator followed by addition of an enzyme nucleophile to the resulting double bond (Fig. 8). When subjected to high pH, however, the inactivated enzyme releases a yellow PLP adduct which has been identified as the aldol product of the cofactor and C-3 of pyruvate (9, Fig. 9) as previously prepared by... 

Fig. 3.24. Model of the molecular structure of exocellular mannoproteins produced by yeast. M, mannose Asn, asparagine Ser, serine Thr, threonine GNAc, A-acetyl-glucosamine , phosphate (Llaubdres, 1988)...

The properties of spider silk reflect its interna] molecular structure. All such silk is made of protein, but spiders produce a variety of proteins with which to spin it. Proteins are built of amino acids, but the specific properties of a protein are determined by the variety of amino acids that join together to form the protein chain. Scientists have found six amino acids — namely, glycine, alanine, proline, tyrosine, serine, and glutamine — in spider silk. Chains that have long sequences of alanine units can pack together very closely in what we call beta-sheets,... 

Fig. 1 Illustrates a further point distances between some compounds are consistent at both concentrations tested, for compounds which are either proximate to one another (alanine, glycine and serine) or distant from one another (e.g. alanine and taurine). As Meredith (23) points out, the persistence of response similarities is explicable in terms of the molecular structure of the three amino acids which differ only in the substitution of -CH and -CH2OH for -H on the -carbon of the glycine. Consequently they may activate the same receptor sites.

Peptidases including keratinases are hydrolases able to hydrolyze peptide bonds in proteins and peptides. They are classified using three different approaches (1) the chemical mechanism of catalysis (based on the catalytic amino acid or metal ion at then-active site, represented by serine, cysteine, threonine, aspartic, asparagine, glutamic and metallocatalytic type), (2) the catalytic reaction (this type of classification depends on the selectivity for the bonds that the peptidases will hydrolyze), and (3) the molecular structure and homology. In this latter approach, amino acid... 

Lesk, A. M., and Fordham, W. D., 1996. Conservation and variability in the structures of serine proteinases of die chymotrypsin family. Journal of Molecular Biology 258 501—537. 

Cholinesterases (ChEs), polymorphic carboxyles-terases of broad substrate specificity, terminate neurotransmission at cholinergic synapses and neuromuscular junctions (NMJs). Being sensitive to inhibition by organophosphate (OP) poisons, ChEs belong to the serine hydrolases (B type). ChEs share 65% amino acid sequence homology and have similar molecular forms and active centre structures [1]. Substrate and inhibitor specificities classify ChEs into two subtypes ... 

SCF, see Self-consistent field treatment (SCF) Schroedinger equation, 2,4,74 Secular equations, 6,10, 52 solution by matrix diagonalization, 11 computer program for, 31-33 Self-consistent field treatment (SCF), of molecular orbitals, 28 Serine, structure of, 110 Serine proteases, 170-188. See also Subtilisin Trypsin enzyme family comparison of mechanisms for, 182-184, 183... 

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