Biomedical subjects

Dennis Madsen

Publications and source records attributed to Dennis Madsen.

6 recordsLinked to original sources

PubMed2006

Using evolutionary information and ancestral sequences to understand the sequence-function relationship in GLP-1 agonists.

Glucagon-like peptide-1 (GLP-1) is an incretin hormone with therapeutic potential for type 2 diabetes. A variety of GLP-1 sequences are known from amphibian species, and some of these have been tested here and found to be able to bind and activate the human GLP-1 receptor. While little difference was observed for the in vitro potency for the human GLP-1 receptor, larger differences were found in the enzymatic stability of these peptides. Two peptides showed increased enzymatic stability, and they group together phylogenetically, though they originate from Amphibia and Reptilia. We have used ancestral sequence reconstruction to analyze the evolution of these GLP-1 molecules, including the synthesis of new peptides. We find that the increased stability could not be observed in the resurrected peptides from the common ancestor of frogs, even though they maintain the ability to activate the human GLP-1 receptor. Another method, using residue mapping on evolutionary branches yielded peptides that had maintained potency towards the receptor and also showed increased stability. This represents a new approach using evolutionary data in protein engineering.

Amino Acid Sequence↗

PubMed2006

New crystal structures of human glutathione transferase A1-1 shed light on glutathione binding and the conformation of the C-terminal helix.

Human glutathione transferase A1-1 is a well studied enzyme, but despite a wealth of structural and biochemical data a number of aspects of its catalytic function are still poorly understood. Here, five new crystal structures of this enzyme are described that provide several insights. Firstly, the structure of a complex of the wild-type human enzyme with glutathione was determined for the first time at 2.0 angstroms resolution. This reveals that glutathione binds in the G site in a very similar fashion as the glutathione portion of substrate analogues in other structures and also that glutathione binding alone is sufficient to stabilize the C-terminal helix of the protein. Secondly, we have studied the complex with a decarboxylated glutathione conjugate that is known to dramatically decrease the activity of the enzyme. The T68E mutant of human glutathione transferase A1-1 recovers some of the activity that is lost with the decarboxylated glutathione, but our structures of this mutant show that none of the earlier explanations of this phenomenon are likely to be correct. Thirdly, and serendipitously, the apo structures also reveal the conformation of the crucial C-terminal region that is disordered in all previous apo structures. The C-terminal region can adopt an ordered helix-like structure even in the apo state, but shows a strong tendency to unwind. Different conformations of the C-terminal regions were observed in the apo states of the two monomers, which suggests that cooperativity could play a role in the activity of the enzyme.

Binding Sites↗

PubMed2006

The effect of neurogenin3 deficiency on pancreatic gene expression in embryonic mice.

To understand the molecular mechanisms regulating pancreatic endocrine development and function, pancreatic gene expression was compared between Ngn3-deficient mice and littermate controls on embryonic days 13 and 15. Microarray analysis identified 504 genes with significant differences in expression. Fifty-two of these showed at least twofold reduction in Ngn3 knockouts compared to controls. Many of them were previously described to be involved in endocrine development and function. Among the genes not previously characterized were Rhomboid veinlet-like 4, genes involved in tetrahydrobiopterin biosynthesis and the Iroquois-type homeobox gene Irx1, the latter was selected for further investigation. In situ hybridisation demonstrated that two Iroquois genes, Irx1 and Irx2, were expressed in pancreatic endoderm of wild-type, but not Ngn3 mutant embryos. Furthermore, ectopic Ngn3 induced prominent Irx2 expression in chicken endoderm. Co-labelling established that Irx1 and Irx2 mRNA is located to glucagon-, but not insulin- or somatostatin-producing cells in mice and chicken. These data suggest that Irx1 and Irx2 serve an evolutionary conserved role in the regulation of alpha-cell-specific gene expression.

Animals↗

PubMed2004

Structures of three salts of phthalic acid; variation in crystal packing and geometry of the hydrogen phthalate ion.

The hydrogen-bond patterns in hydrogen phthalates (HP) have been elucidated by the determination of the crystal structures of hydrogen phthalate salts of [Mg(H(2)O)(4)-(CH(3)OH)(2)](2+), 2-(2'-pyridylamine)pyridinium and diethylammonium. The stoichiometry of the latter salt corresponds to a hydrogen phthalate salt; however, it contains the phthalic acid in its three possible acid-base forms. The hydrogen phthalate ions in the three salts display the two common hydrogen-bonding motifs. One has a very short intramolecular O-H-O hydrogen bond (Intra-H), as seen in the magnesium salt [O...O 2.397 (2) A]. In the other two salts the hydrogen phthalate ions are connected by hydrogen bonds into infinite chains (Chain-H) with O...O distances of 2.460 (1) A in the diethylamine salt and 2.610 (1) A in the 2,2'-dipyridylamine salt. This difference in hydrogen-bond pattern was further elucidated by a search in the Cambridge Structural Database for other hydrogen phthalate salts. Intra-H possesses the shortest O...O distances and an almost planar hydrogen phthalate ion, whereas the hydrogen phthalate ions show significantly more variation in the Chain-H salts. The two hydrogen-bonding motifs are reflected in the molecular geometry of the hydrogen phthalate ion.

Journal Article↗

PubMed2004

The charge density of urea from synchrotron diffraction data.

The charge density of urea is studied using very high precision single-crystal synchrotron-radiation diffraction data collected at the Swiss-Norwegian Beam Lines at ESRF. An unprecedented resolution of 1.44 A(-1) in sin theta;/lambda is obtained at 123 K. The optimization of the experiment for charge-density studies is discussed. The high precision of the data allowed the refinement of a multipole model extending to hexadecapoles and quadrupoles on the heavy and H atoms, respectively, as well as a liberal treatment of radial functions. The topological properties of the resulting electron density are analysed and compared with earlier experimental results as well as with periodic Hartree-Fock calculations. The properties of the strongly polarized C-O bond agree with trends derived from previous experimental results while the ab initio calculations differ significantly. The results indicate that the description of the C-O bond requires more flexible basis sets in the theoretical calculations. The calculated integrated atomic charges are much larger than the observed ones. It is suggested that the present experimental results provide new target values for validation of future ab initio calculations. The molecular dipole moment derived from the integrated atomic properties is the same as the one obtained from the multipole model even though the individual atomic contributions differ. Comparison with literature data for urea in solution and the gas phase yields a dipole enhancement in the solid of about 1.5 D. The thermal expansion of urea is determined using synchrotron powder diffraction data. With decreasing temperature, an increasing anisotropic strain is observed.

Journal Article↗

PubMed2004

Evaluation of protein fold comparison servers.

When a new protein structure has been determined, comparison with the database of known structures enables classification of its fold as new or belonging to a known class of proteins. This in turn may provide clues about the function of the protein. A large number of fold comparison programs have been developed, but they have never been subjected to a comprehensive and critical comparative analysis. Here we describe an evaluation of 11 publicly available, Web-based servers for automatic fold comparison. Both their functionality (e.g., user interface, presentation, and annotation of results) and their performance (i.e., how well established structural similarities are recognized) were assessed. The servers were subjected to a battery of performance tests covering a broad spectrum of folds as well as special cases, such as multidomain proteins, Calpha-only models, new folds, and NMR-based models. The CATH structural classification system was used as a reference. These tests revealed the strong and weak sides of each server. On the whole, CE, DALI, MATRAS, and VAST showed the best performance, but none of the servers achieved a 100% success rate. Where no structurally similar proteins are found by any individual server, it is recommended to try one or two other servers before any conclusions concerning the novelty of a fold are put on paper.

Computational Biology↗