Biomedical subjects

K Diederichs

Publications and source records attributed to K Diederichs.

40 records · Page 3Linked to original sources

PubMed1991

The refined structure of the complex between adenylate kinase from beef heart mitochondrial matrix and its substrate AMP at 1.85 A resolution.

The crystal structure of the complex between adenylate kinase from bovine mitochondrial matrix and its substrate AMP has been refined at 1.85 A resolution (1 A = 0.1 nm). Based on 42,519 independent reflections of better than 10 A resolution, a final R-factor of 18.9% was obtained with a model obeying standard geometry within 0.016 A in bond lengths and 3.2 degrees in bond angles. There are two enzyme: substrate complexes in the asymmetric unit, each consisting of 226 amino acid residues, one AMP and one sulfate ion. A superposition of the two full-length polypeptides revealed deviations that can be described as small relative movements of three domains. Best superpositions of individual domains yielded a residual overall root-mean-square deviation of 0.3 A for the backbone atoms and 0.5 A for the sidechains. The final model contains 381 solvent molecules in the asymmetric unit, 2 x 72 = 144 of which occupy corresponding positions in both complexes.

Adenosine Monophosphate↗

PubMed1990

Three-dimensional structure of the complex between the mitochondrial matrix adenylate kinase and its substrate AMP.

Crystals of adenylate kinase from beef heart mitochondrial matrix (EC 2.7.4.10) complexed with its substrate AMP were analyzed by X-ray diffraction. The crystal structure was solved by multiple isomorphous replacement and solvent flattening at a resolution of 3.0 A. There are two enzyme-substrate molecules in the asymmetric unit. The resolution was extended to 1.9 A by model building and refinement using simulated annealing. The current R-factor is 28.4%. The model is given as a backbone tracing for residues 5-218. The enzyme can be subdivided into three domains, the relative arrangements of which differ slightly but significantly between the two crystallographically independent molecules. When compared with other adenylate kinase structures, the chain fold is similar but the observed domain arrangement differs grossly, suggesting that large parts of the enzyme move during catalysis. The observed binding site of AMP is described. Its location in conjunction with data from homologous proteins clarifies the nucleotide-binding sites of the adenylate kinases. Previous assignments of these sites derived from X-ray crystallographic and nuclear magnetic resonance analyses are discussed.

Adenosine Monophosphate↗

PubMed1990

Induced-fit movements in adenylate kinases.

The high-resolution crystal structures of three homologous adenylate kinases with zero, one and both ( = 2-substrate mimicking inhibitor) bound substrates have been compared. The comparisons are meaningful, because all structures occur in two or three different crystal contact environments indicating that they represent intrinsically stable conformations in solution. Molecular superimpositions revealed that two domains comprising 30 and 38 residues undergo large movements on substrate binding, which can be approximated by rigid-body rotations over 39 degrees and 92 degrees, respectively. Moreover, these movements can be subdivided into two steps: first, a change on binding substrate AMP, which involves only the 30 residue domain (C alpha shifts up to 8.2 A), and second, a change on additional binding of substrate ATP, which again involves the 30 residue domain (C alpha shifts up to 7.6 A) but also the 38 residue domain (C alpha shifts up to 32.3 A). Taken together, these observations yield a three-picture "moving film" of the induced-fit.

Adenosine Monophosphate↗

PubMed1989

Stabilization of detergent-solubilized Ca2+-ATPase by poly(ethylene glycol).

The (Ca2+ + Mg2+)-ATPase from sarcoplasmic reticulum (SR) has been solubilized with 1-alkanoyl propanediol-3-phosphorylcholines with chainlengths ranging between 8 and 12 C atoms. A marked dependence of the ATPase activity upon the chainlength was found, indicating that alkyl chainlengths with 12 C atoms are necessary for retention of activity. Addition of poly(ethylene glycol) to the eluting buffers used for gel filtration of the ATPase-detergent micelles was found to increase the activity and the long-term stability significantly. In the presence of Ca2+, the elution volume indicated an ATPase dimer, whereas in the absence of Ca2+ the elution volume indicated a monomeric solution. The purity of the preparations after gel filtration was improved by subsequent chromatography with a hydroxyapatite column.

Animals↗