Lars Fogh Iversen

Structural and Evolutionary Relationships among Protein Tyrosine Phosphatase Domains

With the current access to the whole genomes of various organisms and the completion of the first draft of the human genome, there is a strong need for a structure-function classification of protein families as an initial step in moving from DNA databases to a comprehensive understanding of human biology. As a result of the explosion in nucleic acid sequence information and the concurrent development of methods for high-throughput functional characterization of gene products, the genomic revolution also promises to provide a new paradigm for drug discovery, enabling the identification of molecular drug targets in a significant number of human diseases. This molecular view of diseases has contributed to the importance of combining primary sequence data with three-dimensional structure and has increased the awareness of computational homology modeling and its potential to elucidate protein function. In particular, when important proteins or novel therapeutic targets are identified—like the family of protein tyrosine phosphatases (PTPs) (reviewed in reference 53)—a structure-function classification of such protein families becomes an invaluable framework for further advances in biomedical science. Here, we present a comparative analysis of the structural relationships among vertebrate PTP domains and provide a comprehensive resource for sequence analysis of phosphotyrosine-specific PTPs.

Heparin-binding protein (HBP/CAP37): a missing link in neutrophil-evoked alteration of vascular permeability.

Polymorphonuclear leukocyte infiltration into tissues in host defense and inflammatory disease causes increased vascular permeability and edema formation through unknown mechanisms. Here, we report the involvement of a paracrine mechanism in neutrophil-evoked alteration in endothelial barrier function. We show that upon neutrophil adhesion to the endothelial lining, leukocytic β2 integrin signaling triggers the release of neutrophil-borne heparin-binding protein (HBP), also known as CAP37/azurocidin, a member of the serprocidin family of neutrophil cationic proteins. HBP induced Ca++-dependent cytoskeletal rearrangement and intercellular gap formation in endothelial-cell monolayers in vitro, and increased macromolecular efflux in microvessels in vivo. Moreover, selective inactivation of HBP prevented the neutrophils from inducing endothelial hyperpermeability. Our data suggest a fundamental role of neutrophil-derived HBP in the vascular response to neutrophil trafficking in inflammation. Targeting this molecule in inflammatory disease conditions offers a new strategy for prevention of endothelial barrier dysfunction caused by misdirected leukocyte activation.

2-(oxalylamino)-benzoic acid is a general, competitive inhibitor of protein-tyrosine phosphatases.

Protein-tyrosine phosphatases (PTPs) are critically involved in regulation of signal transduction processes. Members of this class of enzymes are considered attractive therapeutic targets in several disease states, e.g. diabetes, cancer, and inflammation. However, most reported PTP inhibitors have been phosphorus-containing compounds, tight binding inhibitors, and/or inhibitors that covalently modify the enzymes. We therefore embarked on identifying a general, reversible, competitive PTP inhibitor that could be used as a common scaffold for lead optimization for specific PTPs. We here report the identification of 2-(oxalylamino)-benzoic acid (OBA) as a classical competitive inhibitor of several PTPs. X-ray crystallography of PTP1B complexed with OBA and related non-phosphate low molecular weight derivatives reveals that the binding mode of these molecules to a large extent mimics that of the natural substrate including hydrogen bonding to the PTP signature motif. In addition, binding of OBA to the active site of PTP1B creates a unique arrangement involving Asp181, Lys120, and Tyr46. PTP inhibitors are essential tools in elucidating the biological function of specific PTPs and they may eventually be developed into selective drug candidates. The unique enzyme kinetic features and the low molecular weight of OBA makes it an ideal starting point for further optimization.

Hospital admissions before and after shipyard closure.

To determine the effect of job loss on health an investigation was made of admissions to hospitals in 887 men five years before and three years after the closure of a Danish shipyard. The control group comprised 441 men from another shipyard. The information on hospital admissions was obtained from the Danish national register of patients. The relative risk of admission in the control group dropped significantly in terms of the number of men admitted from the study group from 1.29 four to five years before closure to 0.74 in the three years after closure. This was especially true of admissions due to accidents (1.33 to 0.46) and diseases of the digestive system (4.53 to 1.03). For diseases of the circulatory system, particularly cardiovascular diseases, the relative risk increased from 0.8 to 1.60, and from 1.0 to 2.6 respectively. These changes in risk of illness after redundancy are probably a consequence of a change from the effects of a high risk work environment to the effects of psychosocial stresses such as job insecurity and unemployment.

Ligand-Induced Conformational Changes: Improved Predictions of Ligand Binding Conformations and Affinities

A computational docking strategy using multiple conformations of the target protein is discussed and evaluated. A series of low molecular weight, competitive, nonpeptide protein tyrosine phosphatase inhibitors are considered for which the x-ray crystallographic structures in complex with protein tyrosine phosphatase 1B (PTP1B) are known. To obtain a quantitative measure of the impact of conformational changes induced by the inhibitors, these were docked to the active site region of various structures of PTP1B using the docking program FlexX. Firstly, the inhibitors were docked to a PTP1B crystal structure cocrystallized with a hexapeptide. The estimated binding energies for various docking modes as well as the RMS differences between the docked compounds and the crystallographic structure were calculated. In this scenario the estimated binding energies were not predictive inasmuch as docking modes with low estimated binding energies corresponded to relatively large RMS differences when aligned with the corresponding crystal structure. Secondly, the inhibitors were docked to their parent protein structures in which they were cocrystallized. In this case, there was a good correlation between low predicted binding energy and a correct docking mode. Thirdly, to improve the predictability of the docking procedure in the general case, where only a single target protein structure is known, we evaluate an approach which takes possible protein side-chain conformational changes into account. Here, side chains exposed to the active site were considered in their allowed rotamer conformations and protein models containing all possible combinations of side-chain rotamers were generated. To evaluate which of these modeled active sites is the most likely binding site conformation for a certain inhibitor, the inhibitors were docked against all active site models. The receptor rotamer model corresponding to the lowest estimated binding energy is taken as the top candidate. Using this protocol, correct inhibitor binding modes could successfully be discriminated from proposed incorrect binding modes. Moreover, the ranking of the estimated ligand binding energies was in good agreement with experimentally observed binding affinities.

Water-molecule network and active-site flexibility of apo protein tyrosine phosphatase 1B

Protein tyrosine phosphatase 1B (PTP1B) plays a key role as a negative regulator of insulin and leptin signalling and is therefore considered to be an important molecular target for the treatment of type 2 diabetes and obesity. Detailed structural information about the structure of PTP1B, including the conformation and flexibility of active-site residues as well as the water-molecule network, is a key issue in understanding ligand binding and enzyme kinetics and in structure-based drug design. A 1.95 A apo PTP1B structure has been obtained, showing four highly coordinated water molecules in the active-site pocket of the enzyme; hence, the active site is highly solvated in the apo state. Three of the water molecules are located at positions that approximately correspond to the positions of the phosphate O atoms of the natural substrate phosphotyrosine and form a similar network of hydrogen bonds. The active-site WPD-loop was found to be in the closed conformation, in contrast to previous observations of wild-type PTPs in the apo state, in which the WPD-loop is open. The closed conformation is stabilized by a network of hydrogen bonds. These results provide new insights into and understanding of the active site of PTP1B and form a novel basis for structure-based inhibitor design.

AGE AND THE OPERATIONALIZATION OF SOCIAL SUPPORT

In most studies social network is operationalized without any consideration of age. But it is to be expected that both the prevalence and the impact on health of the various sources of social support change through life. If this is true, then the use of a global index may lead to distorted results regarding age changes of the social network. In a cross-sectional study of 1500 occupationally active, Danish men aged 16-74, the hypothesized age dependencies were studied with health operationalized as psychological well-being and social support divided into support from wife, children, family and friends. The prevalence of support from the wife increased with age, whereas her impact on health was only significantly positive in the age range 30-49. Support from family and friends was most prevalent among the youngest, but it had a positive impact on health both among the young and the old. The results regarding impact on health are corroborated by two other studies on mortality. These findings point to methodological errors that may distort results when global network measures are used irrespective of the ages of the participants studied.

Residue 182 influences the second step of protein-tyrosine phosphatase-mediated catalysis.

Previous enzyme kinetic and structural studies have revealed a critical role for Asp181 (PTP1B numbering) in PTP (protein-tyrosine phosphatase)-mediated catalysis. In the E-P (phosphoenzyme) formation step, Asp181 functions as a general acid, while in the E-P hydrolysis step it acts as a general base. Most of our understanding of the role of Asp181 is derived from studies with the Yersinia PTP and the mammalian PTP1B, and to some extent also TC (T-cell)-PTP and the related PTPa and PTPe. The neighbouring residue 182 is a phenylalanine in these four mammalian enzymes and a glutamine in Yersinia PTP. Surprisingly, little attention has been paid to the fact that this residue is a histidine in most other mammalian PTPs. Using a reciprocal single-point mutational approach with introduction of His182 in PTP1B and Phe182 in PTPH1, we demonstrate here that His182-PTPs, in comparison with Phe182-PTPs, have significantly decreased kcat values, and to a lesser degree, decreased kcat/Km values. Combined enzyme kinetic, X-ray crystallographic and molecular dynamics studies indicate that the effect of His182 is due to interactions with Asp181 and with Gln262. We conclude that residue 182 can modulate the functionality of both Asp181 and Gln262 and therefore affect the E-P hydrolysis step of PTP-mediated catalysis.

Atomic resolution structure of human HBP/CAP37/azurocidin.

Crystals of human heparin binding protein (HBP) diffract to 1.1 A when flash-frozen at 120 K. The atomic resolution structure has been refined anisotropically using SHELXL96. The final model of HBP consists of 221 amino-acid residues of 225 possible, three glycosylation units, one chloride ion, 15 precipitant ethanol molecules and 323 water molecules. The structure is refined to a final crystallographic R factor of 15.9% and Rfree(5%) of 18.9% using all data. A putative protein kinase C activation site has been identified, involving residues 113-120. The structure is compared to the previously determined 2.3 A resolution structure of HBP.

Participation in a follow up study of health among unemployed and employed people after a company closedown: drop outs and selection bias.

This article presents an analysis of study loss in a three year longitudinal study of 1816 employees at two Danish shipyards, one of which closed just before the start of the study. The aim of the study was to elucidate the health consequences of a company closedown and the subsequent job loss. The study population responded to an identical questionnaire in 1983, 1984 and 1985. The participation rate in 1983 was 73%. The percentage of drop outs in 1984 and 1985 was 15-20% of the total numbers responding in the first year. We examined this study loss in relation to the characteristics of the respondents, using the first round of data collection as a baseline. In a multivariate analysis, age and seniority at the shipyard were the only variables that were significantly associated with non-participation in 1984 and 1985. It is concluded that the drop outs did not appear to introduce a serious risk of selection bias in 1984 and 1985. A comparison between drop outs and late respondents in 1984 and 1985 did not support the supposition that information about late respondents can be extrapolated to drop outs.