![]() Instead of representing motion, they represent poses - motion must be inferred. Unfortunately, they are not well suited for conveying molecular motion and variations in molecular motion to users. Such representations can be used in full 3D interactive modalities, as well as in 2D modes, and can easily be animated by simply playing each pose in sequence. In such representations, each overlaid pose represents the physical state of the molecule at a discrete moment in time. Traditionally, visual representations of molecular motion have consisted simply of displaying these snapshots as a series of static images, often overlaid upon each other, similar to stroboscopic multiple-exposure pictures of motion. Nuclear Magnetic Resonance imaging (NMR) or Molecular Dynamics simulations (MD) can yield snapshots of molecular conformations that represent changes in the structure of a molecule over time. To understand the similarities and differences between different molecular motions (of the same molecule, or between different molecules): "These all moved similarly, while that mutant takes a different path".Īddressing these needs requires a representation that promotes motion to the primary feature being conveyed, rather than representing conformations as the primary feature and requiring interpretation to recognize motion. To understand timing and speed: "It spent a long time, here, then quickly moved there". "It moved from here to there", versus "it jiggled about". To differentiate (largely) ordered motion from (largely) unordered motion. To quickly identify regions of significant motion and of little motion: "This moved, that didn't". To quickly acquire a qualitative overall understanding of a molecular motion: "It moved like this". Current analytical methods are producing ever more data that can help answer questions about conformational flexibility for these non-molecular-biologist users, yet current visualization tools are targeted to the quantitative molecular biologist, rather than their end-customer who needs to understand, rather than measure the motion. This phenomenon is a source of fascination for the molecular biologist who wishes to understand how and why the dynamics affect function, but it is a frustration for the virologist who wants to know whether an antibody blocks a folding event, the gene therapist who wants to know where she can modify a delivery vector without altering its necessary mechanics, and the microbiologist trying to understand how a seemingly innocuous change to an anti-microbial peptide produces a surprisingly large change in efficacy. Justification for the needĪs more detail is uncovered about protein structures and their flexibility, it is often found that the dynamics of conformation changes - not simply the alternate conformations themselves, but the molecular motion, the paths taken between conformations and the frequency with which different molecules take different paths - play a part in modulating the molecular functionality. We also introduce a web resource that enables users to construct these representations from their own data, in a 2D projection form, a 3D virtual model form, and also a 3D-printable form. In this manuscript we introduce a sensory-based representation for molecular motion that is aimed at the end-customer basic bio/life-sciences researcher who wants to understand "how did my molecule move", and who wants to be able to make intuitive comparisons between different molecules, without becoming deeply experienced with quantitative molecular biology tools. Molecular biologists who live with them daily do develop facility, but the end-customer biologist is often left bewildered because the representations eschew sensory cues. The atoms of proteins are represented as having single discrete locations and colored by confidence, or the molecule is represented as having a set of discrete, perfectly-known poses, with no representation of transition between them.įluently reading these representations requires considerably user training and experience because they are highly reliant on convention. However, canonical representations for molecular structures and their mobility convey none of this information to the user in an intuitive fashion. To be sure, PDB structure files often contain confidence-level information detailing how much uncertainty is present in the coordinates of the individual atoms, or contain several alternative structures implying that the protein can transition between them. ![]() ![]() Few proteins are as conformationally rigid as their "structures", accessible through the Protein Data Bank (PDB), would imply. ![]()
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |