TY - JOUR
T1 - Detection of non-topological motifs in protein structures
AU - Alesker, Vladimir
AU - Nussinov, Ruth
AU - Wolfson, Haim J.
N1 - Funding Information:
We thank Drs Nikolai Alexandrov, Daniel Fischer, Robert Jemigan and Jacob V.Maizel for helpful discussions, encouragement and interest. We thank the personnel at the Frederick Cancer Research and Development Center for their assistance. The research of R.N. has been sponsored by the National Cancer Institute, DHHS, under contract no. l-CO-74102 with SAIC. The research of H.J.W. has been supported in part by a grant from the Israel Science Foundation administered by the Israel Academy of Sciences. The research of R.N. in Israel has been supported in part by grant no. 91-00219 from the US-Israel Binational Science Foundation (BSF) and by a grant from the Israel Science Foundation administered by the Israel Academy of Sciences. This work formed part of the MSc thesis of V.A., Tel Aviv University. The contents of this publication do not necessarily reflect the views or policies of the DHHS, nor does mention of trade names, commercial products or organizations imply endorsement by the US Government.
PY - 1996/12
Y1 - 1996/12
N2 - We present an efficient technique for the comparison of protein structures. The algorithm uses a vector representation of the secondary structure elements and searches for spatial configurations of secondary structure elements in proteins. In such recurring protein folds, the order of the secondary structure elements in the protein chains is disregarded. The method is based on the geometric hashing paradigm and implements approaches originating in computer vision. It represents and matches the secondary structure element vectors in a 3-D translation and rotation invariant manner. The matching of a pair of proteins takes on average under 3 s on a Silicon Graphics Indigo2 workstation, allowing extensive all-against-all comparisons of the data set of non-redundant protein structures. Here we have carried out such a comparison for a data set of over 500 protein molecules. The detection of recurring topologicai and non-topological, secondary structure element order-independent protein folds may provide further insight into evolution. Moreover, as these recurring folding units are likely to be conformationally favourable, the availability of a data set of such topological motifs can serve as a rich input for threading routines. Below, we describe this rapid technique and the results it has obtained. While some of the obtained matches conserve the order of the secondary structure elements, others are entirely order independent. As an example, we focus on the results obtained for Che Y, a signal transduction protein, and on the profilin-β-actin complex. The Che Y molecule is composed of a five-stranded, parallel β-sheet flanked by five helices. Here we show its similarity with the Escherichia coli elongation factor, with L-arabinose binding protein, with haloalkane dehalogenase and with adenylate kinase. The profilin-β-actin contains an antiparallel β-pleated sheet with α-helical termini. Its similarities to lipase, fructose disphosphatase and β-lactamase are displayed.
AB - We present an efficient technique for the comparison of protein structures. The algorithm uses a vector representation of the secondary structure elements and searches for spatial configurations of secondary structure elements in proteins. In such recurring protein folds, the order of the secondary structure elements in the protein chains is disregarded. The method is based on the geometric hashing paradigm and implements approaches originating in computer vision. It represents and matches the secondary structure element vectors in a 3-D translation and rotation invariant manner. The matching of a pair of proteins takes on average under 3 s on a Silicon Graphics Indigo2 workstation, allowing extensive all-against-all comparisons of the data set of non-redundant protein structures. Here we have carried out such a comparison for a data set of over 500 protein molecules. The detection of recurring topologicai and non-topological, secondary structure element order-independent protein folds may provide further insight into evolution. Moreover, as these recurring folding units are likely to be conformationally favourable, the availability of a data set of such topological motifs can serve as a rich input for threading routines. Below, we describe this rapid technique and the results it has obtained. While some of the obtained matches conserve the order of the secondary structure elements, others are entirely order independent. As an example, we focus on the results obtained for Che Y, a signal transduction protein, and on the profilin-β-actin complex. The Che Y molecule is composed of a five-stranded, parallel β-sheet flanked by five helices. Here we show its similarity with the Escherichia coli elongation factor, with L-arabinose binding protein, with haloalkane dehalogenase and with adenylate kinase. The profilin-β-actin contains an antiparallel β-pleated sheet with α-helical termini. Its similarities to lipase, fructose disphosphatase and β-lactamase are displayed.
KW - Analysis of crystallographic databases
KW - Computer vision
KW - Geometric hashing
KW - Protein structure comparison
KW - Topological motifs
UR - http://www.scopus.com/inward/record.url?scp=0030464952&partnerID=8YFLogxK
U2 - 10.1093/protein/9.12.1103
DO - 10.1093/protein/9.12.1103
M3 - מאמר
AN - SCOPUS:0030464952
VL - 9
SP - 1103
EP - 1119
JO - Protein Engineering, Design and Selection
JF - Protein Engineering, Design and Selection
SN - 1741-0126
IS - 12
ER -