Highly Accurate Structure-Based Prediction of HIV-1 Coreceptor Usage Suggests Intermolecular Interactions Driving Tropism

HIV-1 entry into host cells is mediated by interactions between the V3-loop of viral glycoprotein gp120 and chemokine receptor CCR5 or CXCR4, collectively known as HIV-1 coreceptors. Accurate genotypic prediction of coreceptor usage is of significant clinical interest and determination of the factors driving tropism has been the focus of extensive study. We have developed a method based on nonlinear support vector machines to elucidate the interacting residue pairs driving coreceptor usage and provide highly accurate coreceptor usage predictions. Our models utilize centroid-centroid interaction energies from computationally derived structures of the V3-loop:coreceptor complexes as primary features, while additional features based on established rules regarding V3-loop sequences are also investigated. We tested our method on 2455 V3-loop sequences of various lengths and subtypes, and produce a median area under the receiver operator curve of 0.977 based on 500 runs of 10-fold cross validation. Our study is the first to elucidate a small set of specific interacting residue pairs between the V3-loop and coreceptors capable of predicting coreceptor usage with high accuracy across major HIV-1 subtypes. The developed method has been implemented as a web tool named CRUSH, CoReceptor USage prediction for HIV-1, which is available at http://ares.tamu.edu/CRUSH/

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12

Every two years groups worldwide participate in the Critical Assessment of Protein Structure Prediction (CASP) experiment to blindly test the strengths and weaknesses of their computational methods. CASP has significantly advanced the field but many hurdles still remain, which may require new ideas and collaborations. In 2012 a web-based effort called WeFold, was initiated to promote collaboration within the CASP community and attract researchers from other fields to contribute new ideas to CASP. Members of the WeFold coopetition (cooperation and competition) participated in CASP as individual teams, but also shared components of their methods to create hybrid pipelines and actively contributed to this effort. We assert that the scale and diversity of integrative prediction pipelines could not have been achieved by any individual lab or even by any collaboration among a few partners. The models contributed by the participating groups and generated by the pipelines are publicly available at the WeFold website providing a wealth of data that remains to be tapped. Here, we analyze the results of the 2014 and 2016 pipelines showing improvements according to the CASP assessment as well as areas that require further adjustments and research

Molecular Recognition of CXCR4 by a Dual Tropic HIV-1 gp120 V3 Loop

HIV-1 cell entry is initiated by the interaction of the viral envelope glycoprotein gp120 with CD4, and chemokine coreceptors CXCR4 and CCR5. The molecular recognition of CXCR4 or CCR5 by the HIV-1 gp120 is mediated through the V3 loop, a fragment of gp120. The binding of the V3 loop to CXCR4 or CCR5 determines the cell tropism of HIV-1 and constitutes a key step before HIV-1 cell entry. Thus, elucidating the molecular recognition of CXCR4 by the V3 loop is important for understanding HIV-1 viral infectivity and tropism, and for the design of HIV-1 inhibitors. We employed a comprehensive set of computational tools, predominantly based on free energy calculations and molecular-dynamics simulations, to investigate the molecular recognition of CXCR4 by a dual tropic V3 loop. We report what is, to our knowledge, the first HIV-1 gp120 V3 loop:CXCR4 complex structure. The computationally derived structure reveals an abundance of polar and nonpolar intermolecular interactions contributing to the HIV-1 gp120:CXCR4 binding. Our results are in remarkable agreement with previous experimental findings. Therefore, this work sheds light on the functional role of HIV-1 gp120 V3 loop and CXCR4 residues associated with HIV-1 coreceptor activity

Intermolecular Interaction Free Energies of V3 loop Residues in Complex with CCR5/CXCR4;

<p>Average intermolecular interaction free energies (y-axis) of V3 loop residues (x-axis). The intermolecular interaction free energies for every V3 loop residue are summed up for all interacting residues of CCR5 (first bar per residue) and CXCR4 (second bar per residue). The polar contribution is denoted in red and green color, for CCR5 and CXCR4, respectively, and the non-polar contribution is denoted in blue and black color, for CCR5 and CXCR4, respectively. The total interaction free energy of each V3 loop residue corresponds to the sum of polar and non-polar contributions.</p

Important intermolecular polar and non-polar interaction free energies, hydrogen bonds, salt bridges, between V3 loop and CCR5 residue pairs within the MD simulation of the complex with the lowest average binding free energy (see <i>Methods</i>).

<p>Important intermolecular polar and non-polar interaction free energies, hydrogen bonds, salt bridges, between V3 loop and CCR5 residue pairs within the MD simulation of the complex with the lowest average binding free energy (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095767#s2" target="_blank"><i>Methods</i></a>).</p

Molecular Recognition of CCR5 by an HIV-1 gp120 V3 Loop

<div><p>The binding of protein HIV-1 gp120 to coreceptors CCR5 or CXCR4 is a key step of the HIV-1 entry to the host cell, and is predominantly mediated through the V3 loop fragment of HIV-1 gp120. In the present work, we delineate the molecular recognition of chemokine receptor CCR5 by a dual tropic HIV-1 gp120 V3 loop, using a comprehensive set of computational tools predominantly based on molecular dynamics simulations and free energy calculations. We report, what is to our knowledge, the first complete HIV-1 gp120 V3 loop : CCR5 complex structure, which includes the whole V3 loop and the N-terminus of CCR5, and exhibits exceptional agreement with previous experimental findings. The computationally derived structure sheds light into the functional role of HIV-1 gp120 V3 loop and CCR5 residues associated with the HIV-1 coreceptor activity, and provides insights into the HIV-1 coreceptor selectivity and the blocking mechanism of HIV-1 gp120 by maraviroc. By comparing the binding of the specific dual tropic HIV-1 gp120 V3 loop with CCR5 and CXCR4, we observe that the HIV-1 gp120 V3 loop residues 13–21, which include the tip, share nearly identical structural and energetic properties in complex with both coreceptors. This result paves the way for the design of dual CCR5/CXCR4 targeted peptides as novel potential anti-AIDS therapeutics.</p></div

HIV-1 gp120 V3 loop : CCR5 Complex Structure;

<p>Molecular graphics image of the entire simulation system corresponding to the complex with the lowest average binding free energy. The V3 loop is shown in tube and transparent surface representation in red color, and the residue moiety 16–20 is shown in fat tube representation. The CCR5 is shown in cartoon representation, and the coloring used for different protein domains is as follows: (i) N-terminal domain is colored in blue, (ii) Transmembrane helix 1 (TH1) is colored in green; (iii) Intracellular loop 1 (ICL1) is colored in light gray; (iv) TH2 is colored in purple, (v) Extracellular loop 1 (ECL1) is colored in light gray; (vi) TH3 is colored in yellow; (vii) ICL2 is colored in light gray; (viii) TH4 is colored in gray; (ix) ECL2 is colored in ochre; (x) TH5 is colored in pink; (xi) ICL3 is colored in light gray; (xii) TH6 is colored in cyan; (xiii) ECL3 is colored in lime; (xiv) TH7 is colored in orange; (xv) C-terminal domain is colored in light gray. The N-terminal Cα atom of CCR5 is shown in a small van der Waals sphere and the V3 loop disulfide bridge is shown in fat transparent licorice representation. The definition of CCR5 and V3 loop domains is presented in <i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095767#pone.0095767.s004" target="_blank">Information S4</a></i>.</p

Elucidating a Key Component of Cancer Metastasis: CXCL12 (SDF-1α) Binding to CXCR4

The chemotactic signaling induced by the binding of chemokine CXCL12 (SDF-1α) to chemokine receptor CXCR4 is of significant biological importance and is a potential therapeutic axis against HIV-1. However, as CXCR4 is overexpressed in certain cancer cells, the CXCL12:CXCR4 signaling is involved in tumor metastasis, progression, angiogenesis, and survival. Motivated by the pivotal role of the CXCL12:CXCR4 axis in cancer, we employed a comprehensive set of computational tools, predominantly based on free energy calculations and molecular dynamics simulations, to obtain insights into the molecular recognition of CXCR4 by CXCL12. We report, what is to our knowledge, the first computationally derived CXCL12:CXCR4 complex structure which is in remarkable agreement with experimental findings and sheds light into the functional role of CXCL12 and CXCR4 residues which are associated with binding and signaling. Our results reveal that the CXCL12 N-terminal domain is firmly bound within the CXCR4 transmembrane domain, and the central 24–50 residue domain of CXCL12 interacts with the upper N-terminal domain of CXCR4. The stability of the CXCL12:CXCR4 complex structure is attributed to an abundance of nonpolar and polar intermolecular interactions, including salt bridges formed between positively charged CXCL12 residues and negatively charged CXCR4 residues. The success of the computational protocol can mainly be attributed to the nearly exhaustive docking conformational search, as well as the heterogeneous dielectric implicit water-membrane-water model used to simulate and select the optimum conformations. We also recently utilized this protocol to elucidate the binding of an HIV-1 gp120 V3 loop in complex with CXCR4, and a comparison between the molecular recognition of CXCR4 by CXCL12 and the HIV-1 gp120 V3 loop shows that both CXCL12 and the HIV-1 gp120 V3 loop share the same CXCR4 binding pocket, as they mostly interact with the same CXCR4 residues

Important Intermolecular Polar Interactions;

<p>Molecular graphics image of important polar interactions corresponding to the complex with the lowest average binding free energy. The figure shows the salt bridges and specific important hydrogen bonds. The V3 loop is shown in tube and in red color, and the residue moiety 16–20 is shown in fat tube representation. The CCR5 is shown in light gray transparent tube representation. The salt bridge and hydrogen bonds are denoted in dashed lines and the participating V3 loop and CCR5 residue moieties are shown in licorice; V3 loop and CCR5 residues are annotated in red and black, color respectively. Hydrogen atoms are omitted for clarity, and the V3 loop disulfide bridge is shown in fat transparent licorice representation.</p