Structural improvement of unliganded simian immunodeficiency virus gp120 core by normal-mode-based X-ray crystallographic refinement

Graduate Program of Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, BCM-125, Houston, TX 77030, USA.
Acta Crystallographica Section D Biological Crystallography (Impact Factor: 2.67). 05/2009; 65(Pt 4):339-47. DOI: 10.1107/S0907444909003539
Source: PubMed


The envelope protein gp120/gp41 of simian and human immunodeficiency viruses plays a critical role in viral entry into host cells. However, the extraordinarily high structural flexibility and heavy glycosylation of the protein have presented enormous difficulties in the pursuit of high-resolution structural investigation of some of its conformational states. An unliganded and fully glycosylated gp120 core structure was recently determined to 4.0 A resolution. The rather low data-to-parameter ratio limited refinement efforts in the original structure determination. In this work, refinement of this gp120 core structure was carried out using a normal-mode-based refinement method that has been shown in previous studies to be effective in improving models of a supramolecular complex at 3.42 A resolution and of a membrane protein at 3.2 A resolution. By using only the first four nonzero lowest-frequency normal modes to construct the anisotropic thermal parameters, combined with manual adjustments and standard positional refinement using REFMAC5, the structural model of the gp120 core was significantly improved in many aspects, including substantial decreases in R factors, better fitting of several flexible regions in electron-density maps, the addition of five new sugar rings at four glycan chains and an excellent correlation of the B-factor distribution with known structural flexibility. These results further underscore the effectiveness of this normal-mode-based method in improving models of protein and nonprotein components in low-resolution X-ray structures.

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    • "Because of the extreme structural flexibility and the heavily N-glycosylation of the protein, establishment of the 3D X-ray structure of its conformational state at a good resolution has presented enormous experimental difficulties. Starting from a structure solved at 4.0 A resolution, a new model was established using a normal mode based refinement method (Chen et al. 2009) (PDB Code 3FUS). Figure 4A shows one representation of the 3D structure of the gp120 glycoprotein where the surface of the protein is displayed using a density grid isosurface approach and the SugarRibbon Fig. 3. Molecular representation of the 3D structure (A) Xanthan polysaccharide, with an illustration of the color coding used to depict the backbone versus the side chain; (B) Starch double helix (left handed parallel stranded) using the SugarRibbon algorithm and the visualization of the ring oxygen atoms. "
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