Quantification of Twist from the Central Lines of β-Strands

Since the discovery of right-handed twist of a β-strand, many studies have been conducted to understand the twist. Given the atomic structure of a protein, twist angles have been defined using atomic positions of the backbone. However, limited study is available to characterize twist when the atomic positions are not available, but the central lines of β-strands are. Recent studies in cryoelectron microscopy show that it is possible to predict the central lines of β-strands from a medium-resolution density map. Accurate measurement of twist angles is important in identification of β-strands from such density maps. We propose an effective method to quantify twist angles from a set of splines. In a data set of 55 pairs of β-strands from 11 β-sheets of 11 proteins, the spline measurement shows comparable results as measured using the discrete method that uses atomic positions directly, particularly in capturing twist angle change along a pair, different levels of twist among different pairs, and the average of twist angles. The proposed method provides an alternative method to characterize twist using the central lines of a β-sheet

Protein Structure Analysis

We describe a series of engaging exercises in which students emulate the process that researchers use to efficiently develop new pharmaceutical drugs, that of rational drug design. The activities are taken from a three- to four-hour workshop regularly conducted with first-year college students and presented here to take place over three to four class periods. Although targeted at college students, these activities may be appropriate at the high school level as well, particularly in an AP Biology course. The exercises introduce students to the topics of bioinformatics and computer modeling, in the context of rational drug design, using free online resources such as databases and computer programs. Through the process of learning about computational drug design and drug optimization, students also learn content such as elements of protein structure and protein–ligand interactions. Based on our assessment, students enjoy the exercises, become more interested in bioinformatics and computer modeling, and demonstrate an increase in content knowledge relevant to the topics

Using α-Helical Coiled-Coils to Design Nanostructured Metalloporphyrin Arrays

We have developed a computational design strategy based on the alpha-helical coiled-coil to generate modular peptide motifs capable of assembling into metalloporphyrin arrays of varying lengths. The current study highlights the extension of a two-metalloporphyrin array to a four-metalloporphyrin array through the incorporation of a coiled-coil repeat unit. Molecular dynamics simulations demonstrate that the initial design evolves rapidly to a stable structure with a small rmsd compared to the original model. Biophysical characterization reveals elongated proteins of the desired length, correct cofactor stoichiometry, and cofactor specificity. The successful extension of the two-porphyrin array demonstrates how this methodology serves as a foundation to create linear assemblies of organized electrically and optically responsive cofactors

PENGEMBANGAN MEDIA PEMBELAJARAN BERBASIS SMARTPHONE PADA MATERI MAKROMOLEKUL PROTEIN

Penelitian ini bertujuan untuk mengembangkan media pembelajaran berbasis smartphone pada materi makromolekul protein. Penelitian ini dilatar belakangi pengguna smartphone yang terus meningkat setiap tahun dan penggunaannya yang berkembang luas, termasuk dalam bidang pendidikan. Kecanggihan smartphone dapat digunakan sebagai sarana dalam mempelajari materi makromolekul protein karena materi ini seringkali dipelajari secara sekilas bahkan terlewat dengan alasan jam pelajaran yang tidak memungkinan untuk dipelajari di akhir semester genap kelas 12 sehingga peserta didik diharuskan mempelajari makromolekul protein secara mandiri. Metode penelitian yang digunakan adalah developmental research dengan model pengembangan menerapkan model pengembangan pembelajaran ADDIE. Media pembelajaran yang diproduksi melalui penelitian ini memiliki 11 gambar, 9 video, dan 1 tabel selain teks yang ditampilkan pada seluruh interface. Media pembelajaran ini layak dari segi media dan materi menurut ahli dan pendidik, sehingga media pembelajaran ini dapat digunakan dalam pembelajaran makromolekul protein. Menurut peserta didik media pembelajaran ini menarik untuk digunakan, memudahkan pemahaman, dan membangkitkan rasa ingin tahu dalam mempelajari materi makromolekul protein. This research aims to develop smartphone-based teaching material on protein macromolecule. This research is in conjunction with the backdrop of smartphone users who continue to increase every year and their widespread use, including in the field of education. The sophistication of smartphones can be used as a medium of studying protein macromolecule because this topic is often studied at a glance even missed on the grounds of hours of lessons that are not possible to be studied at the end of the semester even grade 12 so that students are required to study protein macromolecules by themself. The research method used is developmental research with implementing ADDIE learning development model. The learning media produced has 11 images, 9 videos, and 1 table in addition to the text displayed on the entire interface. This is feasible in terms of media and subject matter according to expert and educators, so it can be used in teaching protein. According to students this courseware is interesting to use, facilitates understanding, and arouses curiosity in studying protein macromolecule

De Novo Design of a Single Chain Diphenylporphyrin Metalloprotein

We describe the computational design of a single-chain four-helix bundle that noncovalently self-assembles with fully synthetic non-natural porphyrin cofactors. With this strategy, both the electronic structure of the cofactor as well as its protein environment may be varied to explore and modulate the functional and photophysical properties of the assembly. Solution characterization (NMR, UV-vis) of the protein showed that it bound with high specificity to the desired cofactors, suggesting that a uniquely structured protein and well-defined site had indeed been created. This provides a genetically expressed single-chain protein scaffold that will allow highly facile, flexible, and asymmetric variations to enable selective incorporation of different cofactors, surface-immobilization, and introduction of spectroscopic probes