X-ray crystallographic studies of proteins

Palmer, R.A., Niwa, H. (2003). X-ray crystallographic studies of protein-ligand interactions. Biochem. Soc. Trans., 31(Pt5), 973-979. 

The ultimate in structural studies would, of course, involve X-ray crystallographic studies of protein crystals prepared from nonaqueous solvents of the kind that are now being so successfully carried out with certain protein crystals prepared from aqueous media (Kendrew et al., 1961). A priori, there is no reason to exclude the possibility that proteins might be crystallized from pure nonaqueous solvents, although no reports of such attempts have appeared. This is particularly so in view of the fact that in certain pure solvents, proteins appear to exhibit a more highly ordered (helical) conformation than they do in water solution. 

The ability of water to act as both donor and acceptor of hydrogen bonds makes it an excellent mediator in protein-carbohydrate complexes. Results of numerous X-ray crystallographic studies of protein-carbohydrate complexes attest to the pervasiveness of water-mediated hydrogen bonds in protein-carbohydrate interactions. Lectin-bound water molecules are proposed to act as an extension of the protein surface itself [1]. This idea is supported by the fact that water molecules occupy conserved sites in the structures of related lectins [24]. In addition, water molecules can mediate similar hydrogen bonding interactions in the complexes of different proteins with a specific carbohydrate ligand or in complexes of the same lectin with different saccharide ligands [1]. 

Stryer L (1968) Implication of X-ray crystallographic studies of protein structure. Annu Rev Biochem 37 25-50... 

Schlichting, L, et al. Time-resolved x-ray crystallographic study of the conformational change in Ha-ras p21 protein on GTP hydrolysis. Nature 345 309-315,... 

Mayer, S.M., Lawson, D.M., Gormal, C.A., Roe, S.M. and Smith B.E. (1999) New insights into structure-function relationships in nitrogenase A 1.6 A resolution X-ray crystallographic study of Klebsiella pneumoniae MoFe-protein, J. Mol Biol., 292, 871-891. 

Many of the current ideas about the shape of the ferritin molecule are derived from the high resolution x-ray crystallographic studies of Harrison and coworkers (5,6) (Figure 1) on the protein coat of ferritin from the spleen of horses, in which essentially all (> 90%) of the polypeptide subunits are identical. However, protein coats of ferritin from other animals, and indeed from different cells and tissues in the same animal, can be composed of assemblages of similar, but distinct, subunits (3). 

X-Ray crystallographic studies of native human carbonic anhydrase II have been reported at 2.0 A resolution (Eriksson et al, 1986, 1988a). Important active-site residues include Thr-199, Thr-200, Glu-106, His-64, Trp-209, Val-121, Val-143, the zinc ion (liganded by His-94, His-96, and His-119), and the zinc-bound hydroxide ion. A schematic view of the active site is found in Fig. 22. The globular protein has a molecular... 

Liu, J. (2000). X-ray crystallographic studies of two nucleic-acid binding protein/ complex systems and one collagen-like peptide. Ph.D. thesis, Rutgers University. 

Like the other weakly polar interactions, amino-aromatic interactions are a mechanism of protein-ligand binding. Perutz et al. (1986) described a series of X-ray crystallographic studies of drugs and peptides bound to deoxy-Hb A. They characterized an amino-aromatic interaction between the 8+ N8—H group of asparagine-108 with the 8 7r-electron cloud of one of the phenyl rings of bezafibrate (see Fig. 20). 

Following the establishment of a-lactalbumin as a Ca(II)-binding protein and the revision of the sequences of several a-lactalbumins (see above), Shewale et al. (1984) suggested that residues 82, 83, 87, and 88 were probably ligands for the calcium. In fact, the X-ray crystallographic studies of Phillips group showed that three of the predicted residues (82, 87, and 88) were involved. The Ca(II) proved to be seven coordinates in baboon a-lactalbumin In addition to the involvement of the residues shown in Table IX (see also Fig. 8), two water molecules are coordinated. The majority of the c-type lysozymes so far sequenced do not have the residues necessary for the coordination of Ca(II) (Table... 

Lesburg, C. A. and Christianson, D. W., X-ray crystallographic studies of engineered hydrogen bond networks in a protein-zinc binding site, J. Am, Chem. Soc. 117, 6838-6844 (1995). 

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