Amino acids crystal structure

Les.), and Couceiro, de Almeida, and Freire (1953) have localized it histo-chemically in the electrical tissue of Electwphorus electricus L. The distribution of carbonic anhydrase in several tissues of two teleosts and its inhibition in vivo by the sulfonamides have been investigated by Maetz (1953a,b). The presence of cathepsin in the stomachs of various animals including pike and trout has been established by Buchs (1954). A new advance has also been made in the comparative study of pepsin. This enzyme, previously crystallized from salmon (Norris and Elam, 1940), halibut (Eriksen, 1943), and shark (Sprissler, 1942), has now been crystallized from three species of tuna (Norris and Mathies, 1953). These interesting researches have shown that fish pepsins differ in crystal structure, amino acid composition, and specificity from swine or bovine pepsins and show a closer relationship to one another. As pointed out by Velick and Udenfriend (1953), specificity requirements toward substrates are less exacting with extracellular enzymes. 

An interest in the crystals of amino acids and small peptides has reemerged with attention to the dynamic properties of these systems, the subtle kinetic factors determining their crystallization and polymorphism, phase transitions and anisotropic structural response to variation of temperature, pressure and an environment. The systems can serve as a unique interface between biology, chemistry, material science and nanotechnology of immediate and future importance. 

Crystals of several amino-acids and of a few simple peptides and other compounds related to proteins have been analyzed recently by three-dimensional methods. These and other accurate determinations of structure constitute the best experimental sources of information about the dimensions and configuration of the polypeptide chain. The present paper comprises a critical summary of this information— in particular, of the principal structural features of the amide group and the N—H---0 hydrogen bonds, as derived from X-ray diffraction analyses of crystals of amino-acids, peptides, and other organic compounds. 

X-ray diffraction studies of the molecular structure of solid proteins may be divided conveniently into two categories (1) investigations made directly on protein material, both fibrous and crystalline, and (2) determinations of atomic positions in crystals of amino acids and other compounds related to proteins. The former have been reported and discussed in some detail in a recent volume of this series (12), and will be but briefly mentioned here the latter constitute the subject matter of the present paper. The attack on the constitution and configuration of protein molecules and on the forces which hold them together in natural proteins is thus being carried out both from the top and from the bottom. Eecent advances in experimental techniques and in theoretical interpretations encourage the hope that the time is not far distant when these two complementary programs will meet and the detailed structure of many protein molecules will be known and understood. 

Fig. 1. Superposition of three crystal structures of cAMP-dependent protein kinase that show the protein in a closed conformation (straight line), in an intermediate conformation (dashed line), and in an open conformation (broken line). The structures were superimposed on the large lobe. In three locations, arrows identify corresponding amino acid positions in the small lobe.

It can be seen from Table 2 that the intrinsic values of the pK s are close to the model compound value that we use for Cys(8.3), and that interactions with surrounding titratable residues are responsible for the final apparent values of the ionization constants. It can also be seen that the best agreement with the experimental value is obtained for the YPT structure suplemented with the 27 N-terminal amino acids, although both the original YPT structure and the one with the crystal water molecule give values close to the experimentally determined one. Minimization, however, makes the agreement worse, probably because it w s done without the presence of any solvent molecules, which are important for the residues on the surface of the protein. For the YTS structure, which refers to the protein crystallized with an SO4 ion, the results with and without the ion included in the calculations, arc far from the experimental value. This may indicate that con-... 

Crystalline Structures. Crystal shape of amino acids varies widely, for example, monoclinic prisms in glycine and orthorhombic needles in L-alanine. X-ray crystallographic analyses of 23 amino acids have been described (31). L-Glutamic acid crystallizes in two polymorphic forms (a and P) (32), and the a-form is mote facdely handled in industrial processes. The crystal stmeture has been determined (33) and is shown in Figure 1. 

An effective method for localizing causes of redox potentials is to plot the total backbone and side chain contributions to ( ) per residue for homologous proteins as functions of the residue number using a consensus sequence, with insertions treated by summing the contribution of the entire insertion as one residue. The results for homologous proteins should be examined for differences in the contributions to ( ) per residue that correlate with observed redox potential differences. These differences can then be correlated with any other sequence-redox potential data for proteins that lack crystal or NMR structures. In addition, any sequences of homologous proteins that lack both redox potentials and structures should be examined, because residues important in defining the redox potential are likely to have semi-sequence conservation of a few key amino acid types. 

The elegant genetic studies by the group of Charles Yanofsky at Stanford University, conducted before the crystal structure was known, confirm this mechanism. The side chain of Ala 77, which is in the loop region of the helix-turn-helix motif, faces the cavity where tryptophan binds. When this side chain is replaced by the bulkier side chain of Val, the mutant repressor does not require tryptophan to be able to bind specifically to the operator DNA. The presence of a bulkier valine side chain at position 77 maintains the heads in an active conformation even in the absence of bound tryptophan. The crystal structure of this mutant repressor, in the absence of tryptophan, is basically the same as that of the wild-type repressor with tryptophan. This is an excellent example of how ligand-induced conformational changes can be mimicked by amino acid substitutions in the protein. 

The lac repressor monomer, a chain of 360 amino acids, associates into a functionally active homotetramer. It is the classic member of a large family of bacterial repressors with homologous amino acid sequences. PurR, which functions as the master regulator of purine biosynthesis, is another member of this family. In contrast to the lac repressor, the functional state of PurR is a dimer. The crystal structures of these two members of the Lac I family, in their complexes with DNA fragments, are known. The structure of the tetrameric lac repressor-DNA complex was determined by the group of Mitchell Lewis, University of Pennsylvania, Philadelphia, and the dimeric PurR-DNA complex by the group of Richard Brennan, Oregon Health Sciences University, Portland. 

Many biochemical and biophysical studies of CAP-DNA complexes in solution have demonstrated that CAP induces a sharp bend in DNA upon binding. This was confirmed when the group of Thomas Steitz at Yale University determined the crystal structure of cyclic AMP-DNA complex to 3 A resolution. The CAP molecule comprises two identical polypeptide chains of 209 amino acid residues (Figure 8.24). Each chain is folded into two domains that have separate functions (Figure 8.24b). The larger N-terminal domain binds the allosteric effector molecule, cyclic AMP, and provides all the subunit interactions that form the dimer. The C-terminal domain contains the helix-tum-helix motif that binds DNA. 

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