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"This book is about protein structural bioinformatics and how it can help understand and predict protein function. It covers structure-based methods that can assign and explain protein function based on overall folds, characteristics of protein surfaces, occurrence of small 3D motifs, protein-protein interactions and on dynamic properties. Such methods help extract maximum value from new experimental structures, but can often be applied to protein models. The book also, therefore, provides comprehensive coverage of methods for predicting or inferring protein structure, covering all structural classes from globular proteins and their membrane-resident counterparts to amyloid structures and intrinsically disordered proteins. The book is split into two broad sections, the first covering methods to generate or infer protein structure, the second dealing with structure-based function annotation. Each chapter is written by world experts in the field. The first section covers methods ranging from traditional homology modelling and fold recognition to fragment-based ab initio methods, and includes a chapter, new for the second edition, on structure prediction using evolutionary covariance. Membrane proteins and intrinsically disordered proteins are each assigned chapters, while two new chapters deal with amyloid structures and means to predict modes of protein-protein interaction. The second section includes chapters covering functional diversity within protein folds and means to assign function based on surface properties and recurring motifs. Further chapters cover the key roles of protein dynamics in protein function and use of automated servers for function inference. The book concludes with two chapters covering case studies of structure prediction, based respectively on crystal structures and protein models, providing numerous examples of real-world usage of the methods mentioned previously. This book is targeted at postgraduate students and academic researchers. It is most obviously of interest to protein bioinformaticians and structural biologists, but should also serve as a guide to biologists more broadly by highlighting the insights that structural bioinformatics can provide into proteins of their interest."

"ABSTRACTLionfish Pterois volitans merupakan spesies asli ikan di samudra Indonesia-Pasifik. Spesies ini diketahui merupakan salah satu spesies invasif yang destruktif. Invasi dari Lionfish ini memberikan dampak negatif pada ekologi dan kondisi ekonomi dari daerah yang terinvasi. Oleh karena itu, untuk mengurangi jumlah Lionfish di lautan dan untuk menarik masyarakat untuk memanfaatkan Lionfish, studi mengenai manfaat dari Lionfish sangat dibutuhkan. Studi yang pernah ada menyatakan bahwa ekstrak racun dari duri Lionfish memiliki potensi efek sitolitik yang banyak diaplikasikan pada studi antitumor. Penelitian ini bertujuan untuk mendapatkan konsentrasi pelarut ammonium sulfat optimum untuk uji antitumor dan untuk mengetahui potensi antitumor pada ekstrak racun duri Lionfish secara lebih lanjut. Untuk mengetahui potensi antitumor pada racun Lionfish, crude venom Lionfish akan diisolasi dengan ammonium sulfat dan hasilnya akan diujikan pada sel HeLa yang akan menjadi model sel tumor. Hasil uji Lowry dan uji BSLT Brine Shrimp Lethality Test menunjukkan bahwa konsentrasi dan aktivitas protein tertinggi didapatkan dari isolasi protein dengan konsentrasi ammonium sulfat tertinggi. Selain itu, hasil uji MTT Microculture Tetrazolium Salt Assay menunjukkan bahwa hingga konsentrasi ammonium sulfat 80, persentase inhibisi terhadap sel HeLa terbesar didapatkan pada sampel yang diisolasi dengan ammonium sulfat dengan saturasi 60 dan 80. Hasil SDS-PAGE menunjukkan ada beberapa protein yang terkandung pada sampel ekstrak racun Lionfish yang sudah diisolasi. Salah satunya diprediksi memberikan efek antiproliferatif dan antiangiogenesis terhadap sel tumor, sementara yang lainnya diprediksi menginduksi aktivitas proliferasi sel tumor. Hasil dari penelitian menyatakan bahwa ekstrak racun duri Lionfish Pterois volitans memiliki efek antitumor, namun memerlukan purifikasi isolate protein lebih lanjut dan studi lanjutan mengenai protein yang terkandung di dalam ekstrak racun Lionfish yang dapat meningkatkan aktivitas antitumor.

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ABSTRACTLionfish Pterois volitans is a native species of Indo Pacific ocean. This species is known as destructive invasive species that invades in many areas, such as Atlantic ocean, the Carribean Sea and the Gulf of Mexico. The invasion of Lionfish gives negative impacts on the ecology and economic condition of the invaded areas. Therefore, to reduce the amount of Lionfish in the ocean and to attract people to exploit Lionfish, the study about Lionfishs benefit is necessary. The recent study revealed that venom extract from Lionfish spines has potential cytolytic effect that is widely used for antitumor studies. In this study, to obtain the optimum concentration of the solvent that used for protein isolation and to observe the antitumor properties of Lionfish further, we isolated the protein of Lionfish venom extract with ammonium sulphate and tested it on HeLa cell as the model of tumor cells. The Lowry and BSLT Brine Shrimp Lethality Test test showed that the highest protein concentration and activity is obtained when crude venom were isolated by the highest concentration of ammonium sulphate. Furthermore, based on the MTT Microculture Tetrazolium Salt assay results, until 80 ammonium sulphate concentration, the greater percentage of inhbition on HeLa cells reached by sample with 60 and 80 percent ammonium sulphate concentration. SDS PAGE results showed that there are several protein contained in the protein isolate of Lionfish venom. One of them is predicted giving antiproliferative and antiangionesis effect to tumor cells, but other is predicted inducing proliferative effect to tumor cells. These results suggest that Lionfish has an antitumor effect, but needs further purification step and more observation about the protein in Lionfish venom extract that can enhance antitumor effect."

"Irbesartan adalah obat golongan penghambat reseptor angiotensin yang diperuntukkan pada pengobatan hipertensi. Irbesartan memiliki indeks terapi yang sempit sehingga kadarnya di dalam darah perlu dipantau. Pemisahan obat dari ikatannya dengan protein plasma merupakan hal yang penting pada analisis obat dalam plasma. Pengendapan protein dalam plasma harus optimum agar analisis berjalan dengan baik. Irbesartan dalam plasma dipisahkan dari ikatannya dengan protein salah satunya dapat dilakukan melalui metode pengendapan protein.Tujuan penelitian ini untuk mendapatkan pengendap protein terbaik dan volume terbaik dengan digunakan beberapa pelarut organik yang dapat bercampur dengan air seperti metanol, etanol, asetonitril, dan aseton. Kondisi optimum dengan hasil area kromatogram paling besar ditunjukkan oleh pelarut etanol dengan penambahan etanol tiga kali dari volume plasma. Analisis irbesartan menggunakan KCKT dengan kolom Kromasil® C18 (5 m; 250 x 4,6 mm), komposisi fase gerak asetonitril-larutan asam format 0,85% pH 3,75 (46:54) (v/v), dan kecepatan alir 1,0 ml/menit. Linearitas yang baik dicapai pada konsentrasi 10,20-5100,00 ng/ml dengan koefisien korelasi (r) 0,9999. LLOQ dari metode yaitu 10,20 ng/ml dan koefesien variasi (KV) 4,47-6,51 %. Nilai % diff selektivitas -11,03-17,63%, uji perolehan kembali relatif 86,19-105,98 %, dan uji perolehan kembali absolut 91,07-118,61 %.

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Irbesartan is an angiotensin receptor blocker intended for treatment of hypertension. Irbesartan has a narrow therapeutic index, so the concentration of irbesartan in human plasma must be monitored. Separation of the drug from its binding with plasma proteins is important in the analysis of drugs in plasma. For the ideal analysis, precipitation of proteins must be optimum. Irbesartan in plasma is separated from its binding with proteins can be done through the method of protein precipitation.

The aims of this study was to obtain optimum protein precipitation and optimum volume used organic solvent which can be mixed with water such as methanol, ethanol, acetonitrile, and acetone. Optimum condition was shown ethanol with the three times volume from plasma to give the large chromatogram?s area. Analysis of irbesartan was conducted by HPLC used Kromasil® C18 column (5 m; 250 x 4,6 mm), mobile phase composition of acetonitrile-formic acid 0,85% pH 3,75 (46:54)(v/v) and flow rate was 1,0 ml/min. Good linearity was obtain at concentrations of 10,20 to 5100,00 ng/ml with a correlation coefficient (r) was 0,9999. LLOQ was 10,20 ng/ml and coefficient variation (CV) was 4,47-6,51%. The value of %diff selectivity was -11,03-17,63%, the relative recovery test was 86,19-105,98%, and absolute recovery was 91,07-118,61%."