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1. Modeling protein–nucleic acid complexes with extremely large conformational changes using Flex‐LZerD

   https://doi.org/10.1002/pmic.202200322  

   Christoffer, Charles; Kihara, Daisuke (December 2022, PROTEOMICS)

   Abstract Proteins and nucleic acids are key components in many processes in living cells, and interactions between proteins and nucleic acids are often crucial pathway components. In many cases, large flexibility of proteins as they interact with nucleic acids is key to their function. To understand the mechanisms of these processes, it is necessary to consider the 3D atomic structures of such protein–nucleic acid complexes. When such structures are not yet experimentally determined, protein docking can be used to computationally generate useful structure models. However, such docking has long had the limitation that the consideration of flexibility is usually limited to small movements or to small structures. We previously developed a method of flexible protein docking which could model ordered proteins which undergo large‐scale conformational changes, which we also showed was compatible with nucleic acids. Here, we elaborate on the ability of that pipeline, Flex‐LZerD, to model specifically interactions between proteins and nucleic acids, and demonstrate that Flex‐LZerD can model more interactions and types of conformational change than previously shown. 

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2. Is Drawing Order Important?

   Qiu, S; Wang, Z; McMillan, L; Rushmeier, H; Dorsey, J (May 2023, Proceedings of EUROGRAPHICS - Short Papers)

   Babaei, V; Skouras, M (Ed.)

   The drawing process is crucial to understanding the final result of a drawing. There has been a long history of understanding human drawing; what kinds of strokes people use and where they are placed. An area of interest in Artificial Intelligence is developing systems that simulate human behavior in drawing. However, there has been little work done to understand the order of strokes in the drawing process. Without sufficient understanding of natural drawing order, it is difficult to build models that can generate natural drawing processes. In this paper, we present a study comparing multiple types of stroke orders to confirm findings from previous work and demonstrate that multiple orderings of the same set of strokes can be perceived as human-drawn and different stroke order types achieve different perceived naturalness depending on the type of image prompt. 

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3. Transliteration of synthetic genetic enzymes

   https://doi.org/10.1093/nar/gkab923  

   Wang, Yajun; Liu, Xiaolin; Shehabat, Mouhamad; Chim, Nicholas; Chaput, John C. (October 2021, Nucleic Acids Research)

   Abstract Functional nucleic acids lose activity when their sequence is prepared in the backbone architecture of a different genetic polymer. The only known exception to this rule is a subset of aptamers whose binding mechanism involves G-quadruplex formation. We refer to such examples as transliteration—a synthetic biology concept describing cases in which the phenotype of a nucleic acid molecule is retained when the genotype is written in a different genetic language. Here, we extend the concept of transliteration to include nucleic acid enzymes (XNAzymes) that mediate site-specific cleavage of an RNA substrate. We show that an in vitro selected 2′-fluoroarabino nucleic acid (FANA) enzyme retains catalytic activity when its sequence is prepared as α-l-threofuranosyl nucleic acid (TNA), and vice versa, a TNA enzyme that remains functional when its sequence is prepared as FANA. Structure probing with DMS supports the hypothesis that FANA and TNA enzymes having the same primary sequence can adopt similarly folded tertiary structures. These findings provide new insight into the sequence-structure-function paradigm governing biopolymer folding. 

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4. RNA fold prediction by Monte Carlo in graph space and the statistical mechanics of tertiary interactions

   https://doi.org/10.1261/rna.080216.124  

   Phan, Ethan NH; Mak, Chi H (December 2024, RNA)

   Using a graph representation of RNA structures, we have studied the ensembles of secondary and tertiary graphs of two sets of RNA with Monte Carlo simulations. The first consisted of 91 target ribozyme and riboswitch sequences of moderate lengths (<150 nt) having a variety of secondary, H-type pseudoknots and kissing loop interactions. The second set consisted of 71 more diverse sequences across many RNA families. Using a simple empirical energy model for tertiary interactions and only sequence information for each target as input, the simulations examined how tertiary interactions impact the statistical mechanics of the fold ensembles. The results show that the graphs proliferate enormously when tertiary interactions are possible, producing an entropic driving force for the ensemble to access folds having tertiary structures even though they are overall energetically unfavorable in the energy model. For each of the targets in the two test sets, we assessed the quality of the model and the simulations by examining how well the simulated structures were able to predict the native fold, and compared the results to fold predictions from ViennaRNA. Our model generated good or excellent predictions in a large majority of the targets. Overall, this method was able to produce predictions of comparable quality to Vienna, but it outperformed Vienna for structures with H-type pseudoknots. The results suggest that while tertiary interactions are predicated on real-space contacts, their impacts on the folded structure of RNA can be captured by graph space information for sequences of moderate lengths, using a simple tertiary energy model for the loops, the base pairs, and base stacks. 

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5. Simple Topological Drawings of k-Planar Graphs.

   https://doi.org/10.1007/978-3-030-68766-3_31  

   Hoffmann, Michael; Liu, Chih-Hung; Reddy, Meghana M.; Toth, Csaba D. (February 2021, Graph Drawing and Network Visualization)

   null (Ed.)

   Every finite graph admits a simple (topological) drawing, that is, a drawing where every pair of edges intersects in at most one point. However, in combination with other restrictions simple drawings do not universally exist. For instance, k-planar graphs are those graphs that can be drawn so that every edge has at most k crossings (i.e., they admit a k-plane drawing). It is known that for k≤3 , every k-planar graph admits a k-plane simple drawing. But for k≥4 , there exist k-planar graphs that do not admit a k-plane simple drawing. Answering a question by Schaefer, we show that there exists a function Open image in new window such that every k-planar graph admits an f(k)-plane simple drawing, for all Open image in new window. Note that the function f depends on k only and is independent of the size of the graph. Furthermore, we develop an algorithm to show that every 4-planar graph admits an 8-plane simple drawing. 

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