TITLE

Three dimensional shape comparison of flexible proteins using the local-diameter descriptor

AUTHOR(S)
Yi Fang; Yu-Shen Liu; Ramani, Karthik
PUB. DATE
January 2009
SOURCE
BMC Structural Biology;2009, Vol. 9, Special section p1
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: Techniques for inferring the functions of the protein by comparing their shape similarity have been receiving a lot of attention. Proteins are functional units and their shape flexibility occupies an essential role in various biological processes. Several shape descriptors have demonstrated the capability of protein shape comparison by treating them as rigid bodies. But this may give rise to an incorrect comparison of flexible protein shapes. Results: We introduce an efficient approach for comparing flexible protein shapes by adapting a local diameter (LD) descriptor. The LD descriptor, developed recently to handle skeleton based shape deformations [1], is adapted in this work to capture the invariant properties of shape deformations caused by the motion of the protein backbone. Every sampled point on the protein surface is assigned a value measuring the diameter of the 3D shape in the neighborhood of that point. The LD descriptor is built in the form of a one dimensional histogram from the distribution of the diameter values. The histogram based shape representation reduces the shape comparison problem of the flexible protein to a simple distance calculation between 1D feature vectors. Experimental results indicate how the LD descriptor accurately treats the protein shape deformation. In addition, we use the LD descriptor for protein shape retrieval and compare it to the effectiveness of conventional shape descriptors. A sensitivity-specificity plot shows that the LD descriptor performs much better than the conventional shape descriptors in terms of consistency over a family of proteins and discernibility across families of different proteins. Conclusion: Our study provides an effective technique for comparing the shape of flexible proteins. The experimental results demonstrate the insensitivity of the LD descriptor to protein shape deformation. The proposed method will be potentially useful for molecule retrieval with similar shapes and rapid structure retrieval for proteins. The demos and supplemental materials are available on https://engineering.purdue.edu/PRECISE/LDD.
ACCESSION #
42634732

 

Related Articles

  • Biochemistry matters. Kornberg, Arthur // Nature Structural & Molecular Biology;Jun2004, Vol. 11 Issue 6, p493 

    Discusses the importance of biochemistry in understanding biology. Universality of biochemistry as manifested in the conservation of the functinos and structures of proteins in evolution from bacteria to humans; Biochemical approach of fractionating and isolating enzymes from a cell-free system...

  • A perspective on proteomics: current applications, challenges and potential uses. Muturi, P. W.; Mwololo, J. K.; Munyiri, S. W.; Rubaihayo, P.; Munyua, J. K.; Mgonja, M. Manyasa E.; Kiarie, N. // Agriculture & Biology Journal of North America;2010, Vol. 1 Issue 5, p916 

    Biological sciences are experiencing an ongoing information revolution. Proteome-wide functional classification using bioinformatics approaches is becoming an important method for revealing unknown protein functions. Most successful computational approaches for protein function prediction...

  • An Alternative to the Traditional Western Blot For Recombinant His-tagged Proteins. Morgenthaler, Justin B.; Stephenson, Jason R.; Friesen, Jon A.; Jones, Marjorie A. // American Journal of Biochemistry & Biotechnology;2006, Vol. 2 Issue 4, p146 

    A rapid, inexpensive and sensitive alternative to the traditional Western Blot is presented here. This method is very useful for detection of recombinant 6-his tagged proteins.

  • Cell biology: Border crossing. Bowie, James U. // Nature;1/27/2005, Vol. 433 Issue 7024, p367 

    The article reports about the translocon complex. The translocon decides whether to insert a segment into the membrane by measuring whether the segment best suits a hydrocarbon, interfacial or aqueous environment. The translocating polypeptide segment would find itself able to interact with both...

  • SNAPs.  // Encyclopedic Reference of Molecular Pharmacology;2004, p874 

    A definition of the term "soluble NSF attachment proteins" (SNAPs) is presented. When they were discovered, they were referred to as cofactors for NSF that mediate the membrane binding of NSF in transport assays. The existence of isoforms of SNAPs in mammalian cells is mentioned and information...

  • What's in a Likelihood? Simple Models of Protein Evolution and the Contribution of Structurally Viable Reconstructions to the Likelihood. LAKNER, CLEMENS; HOLDER, MARK T.; GOLDMAN, NICK; NAYLOR, GAVIN J. P. // Systematic Biology;Mar2011, Vol. 60 Issue 2, p161 

    Most phylogenetic models of protein evolution assume that sites are independent and identically distributed. Interactions between sites are ignored, and the likelihood can be conveniently calculated as the product of the individual site likelihoods. The calculation considers all possible...

  • Molecular Beacon Aptamers for Protein Monitoring in Real-Time and in Homogeneous Solutions. Cao, Zehui; Suljak, Steven W.; Weihong Tan // Current Proteomics;Apr2005, Vol. 2 Issue 1, p31 

    Aptamers are nucleic acids selected for binding target molecules of interest with high affinity and selectivity. They have seen increasing application in protein detection due to many of their advantages over traditional protein probes such as antibodies. Aptamers' robust yet flexible functional...

  • What's in a loop? Feller, Stephan M.; Lewitzky, Marc // Cell Communication & Signaling;2012, Vol. 10 Issue 1, p31 

    DNAs and proteins are major classes of biomolecules that differ in many aspects. However, a considerable number of their members also share a common architectural feature that enables the assembly of multi-protein complexes and thereby permits the effective processing of signals: loop structures...

  • Membranes: Shaping biological matter. Frolov, Vadim A.; Zimmerberg, Joshua // Nature Materials;Mar2009, Vol. 8 Issue 3, p173 

    The article discusses the results of studies concerning membranes and the shaping of biological matter. Biological membranes form an extremely dynamic and complex network in cells, guided by specialized protein machinery. One study has developed a novel algorithm that analyzes membrane shape to...

Share

Read the Article

Courtesy of VIRGINIA BEACH PUBLIC LIBRARY AND SYSTEM

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics