Investigation of Carbohydrate Recognition via Computer Simulation.
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.
UT-ORNL Graduate School of Genome Science and Technology, Knoxville, TN 37996, USA. qjohnso3@utk.edu.
Quentin R
QR
Johnson
Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA. rlindsa2@utk.edu.
Richard J
RJ
Lindsay
Center for Molecular Biophysics, Oak Ridge National Lab, Oak Ridge, TN 37830, USA. petridisl@ornl.gov.
Loukas
L
Petridis
Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA. tshen@utk.edu.
Tongye
T
Shen
D000465:Algorithms; D001665:Binding Sites; D050260:Carbohydrate Metabolism / Q000502:physiology*; D002241:Carbohydrates / Q000737:chemistry; D015195:Drug Design; D037102:Lectins / Q000737:chemistry / Q000378:metabolism*; D008954:Models, Biological; D056004:Molecular Dynamics Simulation; D015398:Signal Transduction; D013816:Thermodynamics
D002241:Carbohydrates; D037102:Lectins