13
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: not found

      Analyzing large-scale structural change in proteins: comparison of principal component projection and Sammon mapping.

      1 , ,
      Proteins

      Read this article at

      ScienceOpenPublisherPubMed
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Effective analysis of large-scale conformational transitions in macromolecules requires transforming them into a lower dimensional representation that captures the dominant motions. Herein, we apply and compare two different dimensionality reduction techniques, namely, principal component analysis (PCA), a linear method, and Sammon mapping, which is nonlinear. The two methods are used to analyze four different protein transition pathways of varying complexity, obtained by using either the conjugate peak refinement method or constrained molecular dynamics. For the return-stroke in myosin, both Sammon mapping and PCA show that the conformational change is dominated by a simple rotation of a rigid body. Also, in the case of the T-->R transition in hemoglobin, both methods are able to identify the two main quaternary transition events. In contrast, in the cases of the unfolding transition of staphylococcal nuclease or the signaling switch of Ras p21, which are both more complex conformational transitions, only Sammon mapping is able to identify the distinct phases of motion.

          Related collections

          Author and article information

          Journal
          Proteins
          Proteins
          1097-0134
          0887-3585
          Jul 1 2006
          : 64
          : 1
          Affiliations
          [1 ] Computational Biochemistry, IWR, University of Heidelberg, Heidelberg, Germany.
          Article
          10.1002/prot.20981
          16617427
          343a51ac-52f3-4797-9911-950ad1e6ecb3
          (c) 2006 Wiley-Liss, Inc.
          History

          Comments

          Comment on this article