Protein Science Sheba protein
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
QUICK SEARCH:   [advanced]


     

This Article
Right arrow Full Text (PDF)
Right arrow Data Supplement
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by ALEXANDROV, N. N.
Right arrow Articles by GO, N.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by ALEXANDROV, N. N.
Right arrow Articles by GO, N.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

Protein Science, Vol 3, Issue 6 866-875, Copyright © 1994 by Cold Spring Harbor Laboratory Press

ARTICLE

Biological meaning, statistical significance, and classification of local spatial similarities in nonhomologous proteins

N. N. ALEXANDROV and N. GO
Protein Engineering Research Institute, 5-2-3 Furuedai, Suita, Osaka 565, Japan

We have completed an exhaustive search for the common spatial arrangements of backbone fragments (SARFs) in nonhomologous proteins. This type of local structural similarity, incorporating short fragments of backbone atoms, arranged not necessarily in the same order along the polypeptide chain, appears to be important for protein function and stability. To estimate the statistical significance of the similarities, we have introduced a similarity score. We present several locally similar structures, with a large similarity score, which have not yet been reported. On the basis of the results of pairwise comparison, we have performed hierarchical cluster analysis of protein structures. Our analysis is not limited by comparison of single chains but also includes complex molecules consisting of several subunits. The SARFs with backbone fragments from different polypeptide chains provide a stable interaction between subunits in protein molecules. In many cases the active site of enzymes is located at the same position relative to the common SARFs, implying a function of the certain SARFs as a universal interface of the protein-substrate interaction.
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?


This article has been cited by other articles:


Home page
 Proc. Natl. Acad. Sci. USAHome page
M. Levitt
Growth of novel protein structural data
PNAS, February 27, 2007; 104(9): 3183 - 3188.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
D. Park, S. Lee, D. Bolser, M. Schroeder, M. Lappe, D. Oh, and J. Bhak
Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map)
Bioinformatics, August 1, 2005; 21(15): 3234 - 3240.
[Abstract] [Full Text] [PDF]

Home page
 Protein Sci.Home page
Z. Zhang, S. Kochhar, and M. G. Grigorov
Descriptor-based protein remote homology identification
Protein Sci., February 1, 2005; 14(2): 431 - 444.
[Abstract] [Full Text] [PDF]

Home page
 Protein Eng Des SelHome page
A. Williams, D.R. Gilbert, and D.R. Westhead
Multiple structural alignment for distantly related all {beta} structures using TOPS pattern discovery and simulated annealing
Protein Eng. Des. Sel., December 1, 2003; 16(12): 913 - 923.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Copyright © 1994 by The Protein Society.