A Self-Assisting Protein Folding Model for Teaching Structural Molecular Biology

Self-Assembly, Self-Folding, and Origami: Comparative Design Principles

Self-assembly is usually considered a parallel process while self-folding and origami are usually considered to be serial processes. We believe that these distinctions do not hold in actual experiments. Based upon our experience with 4D printing, we have developed three additional hybrid classes: (1) templated-assisted (tethered) self-assembly: e.g., when RNA is bound to viral capsomeres, the subunits are constricted in their interactions to have aspects of self-folding as well; (2) self-folding can depend upon interactions with the environment; for example, a protein synthesized on a ribosome will fold as soon as peptides enter the intracellular environment in a serial process whereas if denatured complete proteins are put into solution, parallel folding can occur simultaneously; and, (3) in turbulent environments, chaotic conditions continuously alternate processes. We have examined the 43,380 Dürer nets of dodecahedra and 43,380 Dürer nets of icosahedra and their corresponding duals: Schlegel diagrams. In order to better understand models of self-assembly of viral capsids, we have used both geometric (radius of gyration, convex hulls, angles) and topological (vertex connections, leaves, spanning trees, cutting trees, and degree distributions) perspectives to develop design principles for 4D printing experiments. Which configurations fold most rapidly? Which configurations lead to complete polyhedra most of the time? By using Hamiltonian circuits of the vertices of Dürer nets and Eulerian paths of cutting trees of polyhedra unto Schlegel diagrams, we have been able to develop a systematic sampling procedure to explore the 86,760 configurations, models of a T1 viral capsid with 60 subunits and to test alternatives with 4D printing experiments, use of Magforms^TM, and origami models to demonstrate via movies the five processes described above.

Wenxiang 3.0: Evolutionary Visualization of α, π, and 3/10 Helices

Wenxiang diagrams illustrate protein helices as spirals on a plane and thus have the advantage over helical wheels of being planar graphs. Wenxiang 3.0 extends the original version by adding 3 major features: (1) individual amino acid residues can be colored according to their evolutionary conservation in comparative multiple sequence alignments using CONSURF encoding; (2) α, π, and 3/10 helices can be illustrated by overlaying arcs representative of the pitches of these helices; and, (3) the physico-chemical properties of amino acids residues in the protein sequence can be re-presented by colored geometric shapes.

Stable magic angle spinning with Low-Cost 3D-Printed parts

A 3D-printed double-bearing magic angle spinning (MAS) system was developed with a home-built 4.0 mm MAS nuclear magnetic resonance (NMR) probe at 7 T. Various fused deposition modelling 3D printers were used to produce spinning modules of ignorable materials costs for rotors with a diameter of 7.0, 4.0, and 3.5 mm. High-performance MAS experiments on the 4.0 mm-diameter model using a pencil-type ceramic rotor and 3D-printed drive cap resulted in a high-resolution ¹H NMR signal of silicone grease. The 3.5 mm-diameter MAS system reached a spinning frequency of 23 kHz. Furthermore, 3D-printed inserts were designed for various rotor sizes which can isolate the sample from humidity for a duration of more than a week. Single crystal inserts for MAS rotors of commercial probes can readily be printed using two-color printers. Those developments enable customized low-cost MAS NMR for both adapting existing and manufacturing new probes, respectively.

Flexible and modular 3D-printed peptide models

A flexible and modular peptide modeling set was designed using freely available software tools. The set consists of space-filling models of all 20 naturally occurring amino acid side chains and a modular kit for constructing peptides employing C-alpha carbons and amide bond groups. Connectors that allow free rotation about phi and psi angles on the peptide, together with explicit representation of peptide backbone hydrogen bond donor and acceptors allows for the construction of a wide range of protein secondary structure motifs. The space-filling side chain models highlight the steric, acid-base, and polarity of these groups. These models were printed using relatively affordable commercially available fused filament fabrication printers with minimal postprinting processing. Use of these models in student group activities focused on amino acids and protein secondary structural features is described. © 2019 International Union of Biochemistry and Molecular Biology, 47(4):432-437, 2019.

Understanding Cellular Respiration through Simulation Using Lego® as a Concrete Dynamic Model

Out of all the complex systems in science education curricula, cellular respiration is considered to be one of the most complex and abstract processes. Students are known to have low interest and difficulties in conceptual understanding of cellular respiration which provides a challenge for teaching and learning. In this study, we took literature about modelling and teaching and learning cellular respiration as a starting point for the design of a concrete dynamic model in which students (n = 126) use Lego® to simulate the process of cellular respiration. Students used the simulation embedded in the context of finding the efficiency of a sediment battery as a future source of green energy and we tested the effects on conceptual learning and situational interest in an experimental study. Results on conceptual learning show that both experimental and control groups had comparable results in the test. The questions that students in the experimental group asked during enactment, however, gave notice of a focus on both isolated component parts as well as modes of organization at higher organizational levels which is linked to how biologists mechanistically understand complex systems. Both groups report a similar high measure to which the topic is meaningful in real life (situational interest value), whereas the enjoyment (situational interest feeling) was significantly increased in the experimental group. Furthermore, students report specific advantages (e.g., I now understand that one acid chemically changes into another and they do not just transfer atoms) and disadvantages (e.g., time issues).

Rational design to improve activity of the Est3563 esterase from Acinetobacter sp. LMB-5

Acinetobacter sp. strain LMB-5 can produce a kind of esterase degrading phthalate esters. However, low activity of Est3563 esterase limited its large-scale application. In this study, computer-aided simulation mutagenesis was used to improve the esterase activity with a tightened screening library and enlarged success rate. Two positive mutants, P218R and A242R, were obtained with 2.5 and 2.1 folds higher than the WT Est3563 esterase, with 11.96 ± 0.45 U·mg^-1 and 9.90 ± 0.52 U·mg^-1, respectively. With the help of bioinformatics analysis and three-dimensional printing technology, it was found that the mutations could increase the 240-280 residues swing distance and make them deviate from the catalytic pocket. The instability and deviation of these residues on the lid-like structure of the esterase could deteriorate the seal of the binding pocket and expose the active site. Thus, the catalytic efficiency of the mutants became higher. This result demonstrates that the instability and deviation of the lid-like structure could expand the binding pocket of the esterase and enhance the esterase activity.

Perspectives on Structural Molecular Biology Visualization: From Past to Present

Visualization has been a key technology in the progress of structural molecular biology for as long as the field has existed. This perspective describes the nature of the visualization process in structural studies, how it has evolved over the years, and its relationship to the changes in technology that have supported and driven it. It focuses on how technical advances have changed the way we look at and interact with molecular structure, and how structural biology has fostered and challenged that technology.

Assemble-And-Match: A Novel Hybrid Tool for Enhancing Education and Research in Rational Structure Based Drug Design

Rational drug design is the process of finding new medication that can activate or inhibit the biofunction of a target molecule by binding to it and forming a molecular complex. Here, shape and charge complementarities between drug and target are key. To help find effective drug molecules out of a huge pool of possibilities, physical and computer aided tools have been developed. Former offers a tangible experience of the molecular interactions yet lacks measurement and evaluation capabilities. Latter enables accurate and fast evaluations, but does not deliver the interactive tangible experience of physical models. We introduce a novel hybrid model called "Assemble-And-Match" where, we enhance and combine the unique features of the two categories. Assemble-And-Match works based on fabrication of customized molecular fragments using our developed software and a 3D printer. Fragments are hinged to each other in different combinations and form flexible peptide chains, conformable to tertiary structures, to fit in the binding pocket of a (3D printed) target molecule. Through embedded measurement marks, the molecular model is reconstructed in silico and its properties are evaluated. We expect Assemble-And-Match tool can enable combination of visuospatial perception with in silico computational power to aid research and education in drug design.