Motivated proteins: a web application for studying small three-dimensional protein motifs

<b>BACKGROUND:</b> Small loop-shaped motifs are common constituents of the three-dimensional structure of proteins. Typically they comprise between three and seven amino acid residues, and are defined by a combination of dihedral angles and hydrogen bonding partners. The most abundant of these are alphabeta-motifs, asx-motifs, asx-turns, beta-bulges, beta-bulge loops, beta-turns, nests, niches, Schellmann loops, ST-motifs, ST-staples and ST-turns.We have constructed a database of such motifs from a range of high-quality protein structures and built a web application as a visual interface to this. <b>DESCRIPTION:</b> The web application, Motivated Proteins, provides access to these 12 motifs (with 48 sub-categories) in a database of over 400 representative proteins. Queries can be made for specific categories or sub-categories of motif, motifs in the vicinity of ligands, motifs which include part of an enzyme active site, overlapping motifs, or motifs which include a particular amino acid sequence. Individual proteins can be specified, or, where appropriate, motifs for all proteins listed. The results of queries are presented in textual form as an (X)HTML table, and may be saved as parsable plain text or XML. Motifs can be viewed and manipulated either individually or in the context of the protein in the Jmol applet structural viewer. Cartoons of the motifs imposed on a linear representation of protein secondary structure are also provided. Summary information for the motifs is available, as are histograms of amino acid distribution, and graphs of dihedral angles at individual positions in the motifs. <b>CONCLUSION:</b> Motivated Proteins is a publicly and freely accessible web application that enables protein scientists to study small three-dimensional motifs without requiring knowledge of either Structured Query Language or the underlying database schem

Artin t-Motifs

We show that analytically trivial t-motifs satisfy a Tannakian duality, without restrictions on the base field, save for that it be of generic characteristic. We show that the group of components of the t-motivic Galois group coincides with the absolute Galois group of the base field.Comment: To appear in Journal of Number Theor

Contextual Motifs: Increasing the Utility of Motifs using Contextual Data

Motifs are a powerful tool for analyzing physiological waveform data. Standard motif methods, however, ignore important contextual information (e.g., what the patient was doing at the time the data were collected). We hypothesize that these additional contextual data could increase the utility of motifs. Thus, we propose an extension to motifs, contextual motifs, that incorporates context. Recognizing that, oftentimes, context may be unobserved or unavailable, we focus on methods to jointly infer motifs and context. Applied to both simulated and real physiological data, our proposed approach improves upon existing motif methods in terms of the discriminative utility of the discovered motifs. In particular, we discovered contextual motifs in continuous glucose monitor (CGM) data collected from patients with type 1 diabetes. Compared to their contextless counterparts, these contextual motifs led to better predictions of hypo- and hyperglycemic events. Our results suggest that even when inferred, context is useful in both a long- and short-term prediction horizon when processing and interpreting physiological waveform data.Comment: 10 pages, 7 figures, accepted for oral presentation at KDD '1

Evolution of Directed Triangle Motifs in the Google+ OSN

Motifs are a fundamental building block and distinguishing feature of networks. While characteristic motif distribution have been found in many networks, very little is known today about the evolution of network motifs. This paper studies the most important motifs in social networks, triangles, and how directed triangle motifs change over time. Our chosen subject is one of the largest Online Social Networks, Google+. Google+ has two distinguishing features that make it particularly interesting: (1) it is a directed network, which yields a rich set of triangle motifs, and (2) it is a young and fast evolving network, whose role in the OSN space is still not fully understood. For the purpose of this study, we crawled the network over a time period of six weeks, collecting several snapshots. We find that some triangle types display significant dynamics, e.g., for some specific initial types, up to 20% of the instances evolve to other types. Due to the fast growth of the OSN in the observed time period, many new triangles emerge. We also observe that many triangles evolve into less-connected motifs (with less edges), suggesting that growth also comes with pruning. We complement the topological study by also considering publicly available user profile data (mostly geographic locations). The corresponding results shed some light on the semantics of the triangle motifs. Indeed, we find that users in more symmetric triangle motifs live closer together, indicating more personal relationships. In contrast, asymmetric links in motifs often point to faraway users with a high in-degree (celebrities)

Verification of DNA motifs in Arabidopsis using CRISPR/Cas9-mediated mutagenesis.

Transcription factors (TFs) and chromatin-modifying factors (CMFs) access chromatin by recognizing specific DNA motifs in their target genes. Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) has been widely used to discover the potential DNA-binding motifs for both TFs and CMFs. Yet, an in vivo method for verifying DNA motifs captured by ChIP-seq is lacking in plants. Here, we describe the use of clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) to verify DNA motifs in their native genomic context in Arabidopsis. Using a single-guide RNA (sgRNA) targeting the DNA motif bound by REF6, a DNA sequence-specific H3K27 demethylase in plants, we generated stable transgenic plants where the motif was disrupted in a REF6 target gene. We also deleted a cluster of multiple motifs from another REF6 target gene using a pair of sgRNAs, targeting upstream and downstream regions of the cluster, respectively. We demonstrated that endogenous genes with motifs disrupted and/or deleted become inaccessible to REF6. This strategy should be widely applicable for in vivo verification of DNA motifs identified by ChIP-seq in plants

Structural motifs of biomolecules

Biomolecular structures are assemblies of emergent anisotropic building modules such as uniaxial helices or biaxial strands. We provide an approach to understanding a marginally compact phase of matter that is occupied by proteins and DNA. This phase, which is in some respects analogous to the liquid crystal phase for chain molecules, stabilizes a range of shapes that can be obtained by sequence-independent interactions occurring intra- and intermolecularly between polymeric molecules. We present a singularityfree self-interaction for a tube in the continuum limit and show that this results in the tube being positioned in the marginally compact phase. Our work provides a unified framework for understanding the building blocks of biomolecules.Comment: 13 pages, 5 figure