<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Irzan Nurman</style></author><author><style face="normal" font="default" size="100%">Ninik Mudjihartini</style></author><author><style face="normal" font="default" size="100%">Nurhadi Ibrahim</style></author><author><style face="normal" font="default" size="100%">Linda Erlina</style></author><author><style face="normal" font="default" size="100%">Fadilah Fadilah</style></author><author><style face="normal" font="default" size="100%">Muchtaruddin Mansyur</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Predictive Simulation and Functional Insights of Serotonin Transporter: Ligand Interactions Explored through Database Analysis</style></title><secondary-title><style face="normal" font="default" size="100%">Pharmacognosy Journal</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Database Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Functional analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Predictive in silico</style></keyword><keyword><style  face="normal" font="default" size="100%">Serotonin Transporter</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2024</style></year><pub-dates><date><style  face="normal" font="default" size="100%">February 2024</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">16</style></volume><pages><style face="normal" font="default" size="100%">52-59</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p class=&quot;rtejustify&quot;&gt;Through its ability to facilitate the absorption of serotonin into presynaptic neurons, the serotonin transporter, also known as SERT, an essential component in the control of neurotransmission. To discover SERT possible therapeutic application, it is essential to have a solid understanding of its dynamic behavior, ligand interactions, and functional consequences. Within the scope of this investigation, the predictive simulations is crucial to investigate the complexities of SERT to gain a fresh understanding of its operation. We use the 6AWN model to describe the sequence and simulate the behavior of SERT in silico. Within this simulation, we anticipate the conformational changes of SERT and its reaction to ligand binding with paroxetine, cholesterol, dodecyl-beta-D-maltose (DDM), and sodium hydrogen ion. We discover critical residues that are crucial in the interaction between ligands and proteins. They have paroxetine binding to I.172, I.172, Y.176, and F.341 are examples of hydrophobic interactions. Example of hydrogen bonds include A.96 and pi-stacking: F.341. The blockage of the serotonin transporter is the principal mechanism of action that paroxetine has. Cholesterol interacts with SERT W.500, W.500, W.500, W.500, L.504, and A.507, and it also interacts with the outward-facing conformation of this transporter in two different ways. In general, cholesterol interacts with SERT and ligands to stabilize their optimal activity and structure. DDM contact with SERT is also a part of this interaction. R.104, D.328, E.494, Y.495, G.498, P.499, T.503, F.556, L.557, S.559, P.561, Y.579, G.582, T.583, and F.586 are the numbers that are currently in use. Within the context of glucosyl transfer processes, DDM has been utilized as an acceptor. And the interaction of Na with SERT S.263, which causes a change in the structure of SERT. Serotonin transporters are present in the environment.&lt;/p&gt;
</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><work-type><style face="normal" font="default" size="100%">Original Article</style></work-type><section><style face="normal" font="default" size="100%">52</style></section><auth-address><style face="normal" font="default" size="100%">&lt;p class=&quot;rtejustify&quot;&gt;&lt;strong&gt;Irzan Nurman&lt;sup&gt;1,2&lt;/sup&gt;, Ninik Mudjihartini&lt;sup&gt;3&lt;/sup&gt;, Nurhadi Ibrahim&lt;sup&gt;2,4,5&lt;/sup&gt;*, Linda Erlina&lt;sup&gt;6,7&lt;/sup&gt;, Fadilah Fadilah&lt;sup&gt;6,7&lt;/sup&gt;*, Muchtaruddin Mansyur&lt;sup&gt;8&lt;/sup&gt;&lt;/strong&gt;&lt;/p&gt;

&lt;p class=&quot;rtejustify&quot;&gt;&lt;sup&gt;1&lt;/sup&gt;Doctoral Programme Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, 10430, Indonesia&lt;/p&gt;

&lt;p class=&quot;rtejustify&quot;&gt;&lt;sup&gt;2&lt;/sup&gt;Medical Technology Cluster, Indonesian Medical Education and Research Institute (IMERI), Faculty of Medicine, Universitas Indonesia, Jakarta, 10430, Indonesia&lt;/p&gt;

&lt;p class=&quot;rtejustify&quot;&gt;&lt;sup&gt;3&lt;/sup&gt;Department of Biochemistry and Biology Molecular, Faculty of Medicine, Universitas Indonesia, Jakarta, 10430, Indonesia&lt;/p&gt;

&lt;p class=&quot;rtejustify&quot;&gt;&lt;sup&gt;4&lt;/sup&gt;Department of Medical Physiology and Biophysics, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia.&lt;/p&gt;

&lt;p class=&quot;rtejustify&quot;&gt;&lt;sup&gt;5&lt;/sup&gt;Neuroscience and Brain Development Cluster, Indonesian Medical Education and Research Institute (IMERI), Faculty of Medicine, Universitas Indonesia, Jakarta, 10430, Indonesia&lt;/p&gt;

&lt;p class=&quot;rtejustify&quot;&gt;&lt;sup&gt;6&lt;/sup&gt;Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Jakarta, 10430, Indonesia&lt;/p&gt;

&lt;p class=&quot;rtejustify&quot;&gt;&lt;sup&gt;7&lt;/sup&gt;Bioinformatics Core Facilities Cluster, Indonesian Medical Education and Research Institute (IMERI), Faculty of Medicine, Universitas Indonesia, Jakarta, 10430, Indonesia&lt;/p&gt;

&lt;p class=&quot;rtejustify&quot;&gt;&lt;sup&gt;8&lt;/sup&gt;Department of Community Medicine, Faculty of Medicine, Universitas Indonesia, Jakarta, 10310, Indonesia.&lt;/p&gt;
</style></auth-address></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ninik Mudjihartini</style></author><author><style face="normal" font="default" size="100%">Dewi Pratiwi Purba</style></author><author><style face="normal" font="default" size="100%">Fadilah Fadilah</style></author><author><style face="normal" font="default" size="100%">Mohammad Sadikin</style></author><author><style face="normal" font="default" size="100%">Sri Widia A. Jusman</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Isolation and Characterization of Neuroglobin and The Reducing Enzyme Metneuroglobin (Neuroglobin Fe3+) From Bovine Brain Tissue</style></title><secondary-title><style face="normal" font="default" size="100%">Pharmacognosy Journal</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bovine brain tissue</style></keyword><keyword><style  face="normal" font="default" size="100%">Neuroglobin</style></keyword><keyword><style  face="normal" font="default" size="100%">Neuroglobin absorption spectrum</style></keyword><keyword><style  face="normal" font="default" size="100%">Reductase enzyme</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2022</style></year><pub-dates><date><style  face="normal" font="default" size="100%">October 2022</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">14</style></volume><pages><style face="normal" font="default" size="100%">504-510</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p class=&quot;rtejustify&quot;&gt;&lt;strong&gt;Background/Aim:&lt;/strong&gt; The brain uses 20% of the O2 consumed by the body for energy metabolism. In 2000, found a protein that is thought to be a binding O2 in the brain, namely neuroglobin (Ngb). Ngb is a member of the hemoprotein which has a heme group. The iron ion in the haem group can be oxidized, so a reducing enzyme is needed. In this study, the isolation, purification, and characterization of Ngb protein and the reducing enzyme from oxidized neuroglobin (neuroglobin Fe3+) were carried out. &lt;strong&gt;Materials and methods&lt;/strong&gt;: Ngb protein was isolated by fractionation technique using ammonium sulfate 90% saturation, purified by anion exchange chromatography (DEAE Cellulose) and immunoaffinity chromatography, confirmed by SDS-PAGE and Western blot. The metneuroglobin-reducing enzyme was isolated by RIPA lysis buffer, purified by Affi gel blue chromatography, and confirmed by SDS-PAGE.&lt;strong&gt; Results:&lt;/strong&gt; The isolated Ngb obtained has a molecular weight of 17.26 kDa. Spectrum analysis in the wavelength range of 350- 500nm, showed the afternoon peaks of deoxyNgb, oxyNgb, carboxyNgb and metNgb were 415 nm, 405 nm, 405 nm, and 420 nm, respectively. The results of the isolation of the reducing enzymes obtained consisted of 2 parts, namely the matrix-bound eluate (eluate-1) and matrix-bound eluate (eluate-2). SDSPAGE results of eluate-1, eluate-2 and Ngb-free fraction (byproduct of Ngb purification) showed the same 3 bands at a molecular weight of 72.45; 26.84 and 16.33 kDa were suspected as reducing enzymes.&lt;strong&gt; Conclusion: &lt;/strong&gt;The reduction kinetics was tested by reacting the fraction and metNgb and measuring the deoxyNgb uptake formed per unit time. The results of the measurement of the ratio of NgbFe3+ to NgbFe2+ from the free fractions Ngb, eluate-1 and eluate-2, which has the best reducing activity is eluate-1 because it has the best regression value of 0.8769.&lt;/p&gt;
</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><work-type><style face="normal" font="default" size="100%">Original Article</style></work-type><section><style face="normal" font="default" size="100%">504</style></section><auth-address><style face="normal" font="default" size="100%">&lt;p class=&quot;rtejustify&quot;&gt;&lt;strong&gt;Ninik Mudjihartini, Dewi Pratiwi Purba, Fadilah Fadilah, Mohammad Sadikin, Sri Widia A. Jusman&lt;/strong&gt;&lt;/p&gt;

&lt;p class=&quot;rtejustify&quot;&gt;&lt;sup&gt;1&lt;/sup&gt;Department of Biology Molecular and Biochemistry, Faculty of Medicine, Universitas Indonesia, Jakarta, INDONESIA.&lt;/p&gt;

&lt;p class=&quot;rtejustify&quot;&gt;&lt;sup&gt;2&lt;/sup&gt;Center of Hypoxia and Oxidative Stress Studies, Faculty of Medicine, Universitas Indonesia, Jakarta, INDONESIA.&lt;/p&gt;

&lt;p class=&quot;rtejustify&quot;&gt;&lt;sup&gt;3&lt;/sup&gt;Magister Program in Biomedical Sciences, Faculty of Medicine Universitas Indonesia, Jakarta, INDONESIA.&lt;/p&gt;

&lt;p class=&quot;rtejustify&quot;&gt;&lt;sup&gt;4&lt;/sup&gt;Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Jakarta, INDONESIA.&lt;/p&gt;

&lt;p class=&quot;rtejustify&quot;&gt;&lt;sup&gt;5&lt;/sup&gt;Bioinformatics Core Facilities - IMERI, Faculty of Medicine, Universitas Indonesia, Jakarta, INDONESIA.&lt;/p&gt;
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