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Molecules 2015, 20(5), 7700-7718; doi:10.3390/molecules20057700

Investigation of Carbohydrate Recognition via Computer Simulation

1
UT-ORNL Graduate School of Genome Science and Technology, Knoxville, TN 37996, USA
2
Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
3
Center for Molecular Biophysics, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
*
Author to whom correspondence should be addressed.
Academic Editor: Els Van Damme
Received: 12 March 2015 / Revised: 15 April 2015 / Accepted: 15 April 2015 / Published: 28 April 2015
(This article belongs to the Special Issue Protein-Carbohydrate Interactions, and Beyond)
View Full-Text   |   Download PDF [1087 KB, uploaded 28 April 2015]   |  

Abstract

Carbohydrate recognition by proteins, such as lectins and other (bio)molecules, can be essential for many biological functions. Recently, interest has arisen due to potential protein and drug design and future bioengineering applications. A quantitative measurement of carbohydrate-protein interaction is thus important for the full characterization of sugar recognition. We focus on the aspect of utilizing computer simulations and biophysical models to evaluate the strength and specificity of carbohydrate recognition in this review. With increasing computational resources, better algorithms and refined modeling parameters, using state-of-the-art supercomputers to calculate the strength of the interaction between molecules has become increasingly mainstream. We review the current state of this technique and its successful applications for studying protein-sugar interactions in recent years. View Full-Text
Keywords: protein-carbohydrate interaction; binding free energy; molecular dynamics simulation; lectin protein-carbohydrate interaction; binding free energy; molecular dynamics simulation; lectin
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Johnson, Q.R.; Lindsay, R.J.; Petridis, L.; Shen, T. Investigation of Carbohydrate Recognition via Computer Simulation. Molecules 2015, 20, 7700-7718.

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