Guidelines for Homology Modeling of Dopamine, Norepinephrine, and Serotonin Transporters

The human dopamine, norepinephrine, and serotonin transporters (hDAT, hNET, and hSERT) are carriers of neurotransmitters and targets for many drugs. Pioneering works in the past three years to elucidate experimental models of the <i>Drosophila</i> dDAT and human hSERT structures will rapidly impact the field of neuroscience. Here, we evaluated automated homology-based human models of these transporters, employing systematic physics-based, knowledge-based, and empirical-based check. Modeling guidelines were conveyed with attention to the central binding site (S1), secondary binding site (S2), and the extracellular loops EL2 and EL4. Application of new experimental models (dDAT and hSERT) will improve the accuracy of homology models, previously utilizing prokaryotic leucine transporter (LeuT) structure, and provide better predictions of ligand interactions, which is required for understanding of cellular mechanisms and for development of novel therapeutics

Forrest plot showing associations between metallothionein staining and tumors (tumors versus healthy controls).

<p>The result of meta-analysis for particular tumor types displayed instead of individual studies. For more detailed results see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085346#pone-0085346-t001" target="_blank">Table 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085346#pone-0085346-t002" target="_blank">2</a>. Sorted alphabetically by tumor types. Forrest plot displayed as odds ratio and 95% confidence intervals. Red dashed line indicates the result for all tumor types together. OR, odds ratio; CI, confidence interval.</p

Forrest plot of studies reporting the association of metallothionein staining and nodal and distant metastases.

<p>Random effects model used for both outcomes, Relative weight of individual studies displayed in %. For more detailed results see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085346#pone-0085346-t001" target="_blank">Table 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085346#pone-0085346-t002" target="_blank">2</a>. Sorted alphabetically by tumor types. Forrest plot displayed as odds ratio and 95% confidence intervals. Red dashed line indicates the result for all studies together. OR, odds ratio; CI, confidence interval.</p

Association of MT staining and clinicopatological factors. Tumor type not taken into account.

<p>Heterogeneity of studies analyzed using Cochran's Q-test (p-value displayed) and using I². Egger's two-tailed test used for publication bias analysis (p-value displayed). * effect measure is odds ratio, OR, except for survival analysis using hazard ratio, HR. CI, confidence interval</p

Flow chart showing the number of citations retrieved by database searching.

<p>Flow chart showing the number of citations retrieved by database searching.</p

Forrest plot of studies reporting the association of metallothionein staining and tumor grading.

<p>Random effects model used. Relative weight of individual studies displayed in %. For more detailed results see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085346#pone-0085346-t001" target="_blank">Table 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085346#pone-0085346-t002" target="_blank">2</a>. * indicates studies using Gleason grading. Sorted alphabetically by tumor types. Forrest plot displayed as odds ratio and 95% confidence intervals. Red dashed line indicates the result for all studies together. OR, odds ratio; CI, confidence interval.</p

Cancer samples.

<p>The total amount of MT analysed in neuroblastoma cells sensitive (UKF-NB4) and resistant (UKF-B4) to cisplatin. SDS-PAGE band in MT position (300 ng for the control) and chronopotentiograms are displayed as the inset pictures (A). The MT chronopotentiograms of the human blood serum of the patients with the malignant breast tumour and MT amount of the individual patients (B).</p

Flow diagram for identification of relevant studies.

<p>Flow diagram for identification of relevant studies.</p

The effect of tris(2-carboxyethyl)phosphine (TCEP).

<p>Dependences of peak H height of Cys, GSH, GSSG, PC2, BSA (A) and its potential (B) on the different TCEP concentration; the picture in inset: chemical structure of TCEP. The influence of TCEP on CPSA signals of 40 fmol MT (5 µl, C). Dependences of peak H height and potential of 40 fmol MT (5 µl) on different TCEP concentration (D). The peak height 55 000 s/V corresponds to 100% (B).</p

Detection limits of thiols (<i>n</i> = 5) using AdTS CPSA method.

a<p>The linear section dependence of the studied thiol concentration.</p>b<p>The limit of Detection (3 S/N).</p>c<p>The limit of Quantification (10 S/N).</p><p>*Per drop sample (5 µl).</p