Simulations of HIV Capsid Protein Dimerization Reveal the Effect of Chemistry and Topography on the Mechanism of Hydrophobic Protein Association Naiyin.

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Simulations of HIV Capsid Protein Dimerization Reveal the Effect of Chemistry and Topography on the Mechanism of Hydrophobic Protein Association Naiyin Yu, Michael F. Hagan Biophysical Journal Volume 103, Issue 6, Pages 1363-1369 (September 2012) DOI: 10.1016/j.bpj.2012.08.016 Copyright © 2012 Biophysical Society Terms and Conditions

Figure 1 Geometry and chemistry of the CA-C dimerization interface. (A) A space-filling model of one monomer from the CA-C dimer (PDBID 1A43 (46)). The residues that play a significant role in dimerization ((47)) are color-coded according to residue-type: nonpolar in red, polar in green, basic in blue, and acidic in purple. Three residues that play a key role in determining water behavior, Ser-178, Glu-180, and Gln-192 are labeled. (B) A side view of the dimer interface is shown, with Ser-178, Glu-180, and Gln-192 represented by space-filling models and the remainder of CA-C dimer structure shown in ribbon representation. Images created with VMD ((76)). Biophysical Journal 2012 103, 1363-1369DOI: (10.1016/j.bpj.2012.08.016) Copyright © 2012 Biophysical Society Terms and Conditions

Figure 2 Effect of interfacial chemistry on water behavior near isolated CA-C monomers. The distribution of water density fluctuations Pυ(N) is shown as a function of the number of waters N in the evaluation volume υ (pictured on the right in red) in the vicinity of the CA-C dimerization interface. Distributions are shown for WT monomers, monomers with the indicated sets of mutations: E180L, Q192L, and S178A/E180L/Q192L (TM), and a region of bulk water with the same volume as the evaluation region. Biophysical Journal 2012 103, 1363-1369DOI: (10.1016/j.bpj.2012.08.016) Copyright © 2012 Biophysical Society Terms and Conditions

Figure 3 Water density distributions during association of CA-C and a mutant. (A) The evaluation volume υ in red is superposed on the CA-C structure with separation D = 5 Å. (B) The distribution of water density fluctuations Pυ(N) is shown for WT CA-C proteins at separations of D = 4, 4.5, and 5 Å. (C) The distribution of water density fluctuations Pυ(N) is shown during the approach of two S178A/E180L/Q192L (TM) proteins at separations of D = 4, 4.1, and 4.5 Å. For B and C, representative snapshots are shown in which water within 5 Å of both proteins is shown along with one monomer oriented to view the interface in cross section; the solvent accessible surface of the protein is shown, with polar regions colored blue and nonpolar regions colored gray. Biophysical Journal 2012 103, 1363-1369DOI: (10.1016/j.bpj.2012.08.016) Copyright © 2012 Biophysical Society Terms and Conditions

Figure 4 Interfacial chemistry determines water behavior during association. The distribution of water density fluctuations Pυ(N) is shown for a separation of D = 4 Å for (A) WT CA-C proteins and indicated single mutations, and (B) the indicated sets of multiple mutations. Biophysical Journal 2012 103, 1363-1369DOI: (10.1016/j.bpj.2012.08.016) Copyright © 2012 Biophysical Society Terms and Conditions

Figure 5 Distribution of water density fluctuations Pυ(N) is shown for D = 4Å from mutants Q192A/E180A/S178A (TM-A) and Q192A/E180A/S178A/E187A (QM-A). The smaller volume of the substituted ALA residues slightly increases the evaluation volume, leading to a larger mean number of waters than observed for WT (Fig. 4 A). Biophysical Journal 2012 103, 1363-1369DOI: (10.1016/j.bpj.2012.08.016) Copyright © 2012 Biophysical Society Terms and Conditions