The combination of molecular dynamics with crystallography for elucidating protein–ligand interactions: a case study involving peanut lectin complexes with T-antigen and lactose

Pratap, JV and Bradbrook, GM and Reddy, GB and Surolia, A and Raftery, J and Helliwell, JR and Vijayan, M (2001) The combination of molecular dynamics with crystallography for elucidating protein–ligand interactions: a case study involving peanut lectin complexes with T-antigen and lactose. In: Acta Crystallographica Section D, 57 (11). pp. 1584-1594.

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Abstract

Peanut lectin binds T-antigen $[Gal\beta (1–3)GalNAc]$ with an order of magnitude higher affinity than it binds the disaccharide lactose. The crystal structures of the two complexes indicate that the higher affinity for T-antigen is generated by two water bridges involving the acetamido group. Fresh calorimetric measurements on the two complexes have been carried out in the temperature range 280–313K. Four sets of nanosecond molecular-dynamics(MD) simulations, two at 293K and the other two at 313K, were performed on each of the two complexes. At each temperature, two some what different protocols were used to hydrate the complex in the two runs. Two MD runs under slightly different conditions for each complex served to assess the reliability of the approach for exploring protein–ligand interactions. Enthalpies based on static calculations and on MD simulations favour complexation involving T-antigen. The simulations also brought to light ensembles of direct and water-mediated protein–sugar interactions in both the cases. These ensembles provide a qualitative explanation for the temperature dependence of the thermodynamic parameters of peanut lectin–T-antigen interaction and for the results of one of the two mutational studies on the lectin. They also support the earlier conclusion that the increased affinity of peanut lectin for T-antigen compared with that for lactose is primarily caused by additional water bridges involving the acetamido group. The calculations provide a rationale for the observed sugar-binding affinity of one of the two available mutants. Detailed examination of the calculations point to the need for exercising caution in interpreting results of MD simulations: while long simulations are not possible owing to computational reasons, it is desirable to carry out several short simulations with somewhat different initial conditions.

Item Type:	Journal Article
Publication:	Acta Crystallographica Section D
Publisher:	International Union of Crystallography
Additional Information:	Copyright belongs to International Union of Crystallography.
Keywords:	protein–ligand interactions;molecular dynamics;peanut-lectin complexes.
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	17 Sep 2008 12:08
Last Modified:	19 Sep 2010 04:49
URI:	http://eprints.iisc.ac.in/id/eprint/15847

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