Zachary T. Goldstein Week 8

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Week 9 Journal Club Preparation

10 Definitions

  1. Glycosylation: The process of adding sugar units such as in the addition of glycan chains to proteins. An occurrence where a carbohydrate is added to a protein molecule, which can occur in the golgi apparatus. (
  2. Virions: A single virus molecule complete with a coat. (
  3. Chemokine: A chemotactic cytokine released by cells to function in chemotaxis, inflammation, and angiogenesis. (
  4. Immunogenic: Refers to the ability of a substance (antigen) to induce an immune response. (
  5. Annealing: The pairing of complementary dna or rna sequences, via hydrogenbonding, to form a double-stranded molecule. Mostoften used to describe the binding of a short primer or probe. (
  6. Root mean square deviations(RMSD): A measure of difference between values; similarity. (
  7. Proteoglycans: A macromolecule that has a core protein attached covalently to one or more glycosaminoglycan chain (
  8. Dihedral angle: The inclination of two planes that meet at an edge (
  9. Beta-turn: A short stretch of polypeptide chain that allows the main direction of the chain to change. It consists of four amino‐acid residues in which the CO group of residue n is hydrogen bonded to the NH group of residue n + 3. (
  10. Asparagines: A crystalline amino acid found in proteins and in many plants; An amino acid that is a common part of many proteins. (


  1. Introduction
    • It is known that the HIV-1 virus enters human host cells through consecutive interactions with surface cell receptors and one of two chemokine co-receptors (CCR5 or CXCR4).
    • Binding to protein causes conformational change that reveals co-receptor binding site, also known as the V3 loop
    • This V3 loop plays a central role in virus biology and forms a good starting point for analyzing which point on the gene should be targeted for anti-AIDS drugs.
    • Most amino acids within the V3 loop are highly variable, but those found on the end terminals and along the immunogenic tip shows potential conservation and rigidity.
    • Understanding and developing a model of these rigid regions along the gene may provide researchers with a new target for drugs that is constant, which helps guide us through the constantly changing nature of the virus.
    • A good 3D model of these V3 regions could help map where exactly these targets exist within the gene.
    • Getting an exact model has been hard in the past due to a shortage of X-ray and NMR images around the region.
    • Preferences of research are given to HIV subtype B found in North and South America, but computer models of subtype A were created to bridge gap between research data on two different subtypes.
    • Major steps taken in this study:
      • Low energy structures of the amino acid sequences contained in the subtype A V3 region were created, and a most probable confirmation was formed.
      • Elements of secondary structures contained within the V3 region were characterized and analyzed throughout the various loops.
      • Simulated structures were collated with each other and those formed using X-Ray crystallography and NMR spectroscopy to reveal commonalities throughout the structures.
      • Molecular dynamics were computed (MD) and rigid and flexible segments were defined within the region; findings were compared to previous studies.
      • A model molecular docking between the V3 region and FKBP and CycA peptides was performed too observe the V3 regions that stay in contact with the ligands.
  2. Methods
    • Modeling 3D V3 Structures
      • Used knowledge of comparative modeling via Xray crystallography and NMR spectroscopy.
      • MODELLER package used for comparative modeling.
      • Subsets containing 10 best models were selected from each set for energy optimization and final refinement.
      • Lowest energy confirmations were formed using AMBER and TINKER software.
    • Identification of Secondary 3D Structures
      • Standard and non-standard Beta Turns were identified using classification methods from previous work.
    • Comparison of 3D V3 Structures
      • Root Mean Square Deviations were taken in atomic units (cRMSD) for the entire V3 region and segments.
      • Best similarity values fell below 2 Angstroms; smaller A means more similar structure.
    • Molecular Dynamics Computations and Docking Simulations
      • GROMACS package were used for simulations .
      • Every 10 ps geometric parameters of MD structure and energy data was recorded.
      • Model docking used the Hex 4.5 program, 3D structures of 2 peptides were taken from previous studies.
  3. Results
    • Figure 1 displays 3D images of 3 segments along the V3 region. The segments include 3-7, 15-19, 28-32. It shows high structural similarity between segments, supported by the given "largest cMRSD" number not exceeding 2A in any case.
    • Figure 2 displays the most conserved HIV V3 region loop as determined by computer programs. This was generated by comparative modeling based off models in pervious experimental studies. Beta turns and a small helical structure is visible in the structure.
    • Figure 3 displays secondary structures along the V3 loop using best energy confirmations as can be seen in Figure 2. Multiple beta turns (sheets) and helix are determined.
    • Figure 4 relates differences between the 3 segments within the V3 region using cRMSD values representing similarity over time. This figure shows that the 15-19 segment showed the most conservation in structure, while the 3-7 segment showed the least conservation/highest variability.
    • Figure 5 gives the general "turn" formation of the V3 region given average cRMSD values for segments across the region. It displays a closeness between segments 13-17 and 21-23, indicating that those amino acid segments are conserved/more similar than the tip and ends of the region.
    • Figure 6 demonstrates similar patterns of conservation across segments 13-17 and 21-23. The data points are closer in these regions than within and outside the loop, indicating the rigidness of the turn structure through observing aRMSD values.
    • Figure 7 visualizes docking structures of the SA-V3 loop with the CycA and FKBP peptides to identify the regions along the V3 loop that stay in touch with ligands during the docking process. Potential docking segments can be identified in figures 5 and 6.
  4. Conclusions
    • A most probable 3D structure was able to be created based on previous studies and energy conservation ideas.
    • Certain spatial folds were found in all V3 regions, focus of studies was placed on functionally active segments.
    • The main result presented in this paper is that the N and C terminal stretches and Immunogenic tip of the V3 region are highly conserved sites along the gene and may be promising targets for eliciting neutralizing antibody responses, affecting HIV-1 tropism, and immunogenicity of AIDS drugs.
    • Inflexible regions of V3 gene are HIV-1 achilles heel.
    • The significance of this work is it provides a potential strategy for treating HIV and preventing AIDS progression by identifying a potential weakness within the virus. HIV is hard to control because of the immune system's inability to recognize it, but the findings on these conserved regions could provide new drug targets that may show promising results.
    • Some limitations of previous studies included that they did not use 3D modeling, subtype B was studied, and not enough data was collected.
    • The results of this study are very consistent with previous findings. Many models of the V3 region had been created before using X-ray Crystallography and NMR spectroscopy and the models created in this research were consistent with them.
    • Future work should be carried out on other subtypes and subjects to increase data sets and understanding of the region and specifically the N/C terminals and tip.

Presentation Slides

Journal Club Presentation


  • I would like to thank my homework partners User:Matthew K. Oki, User:Mia Huddleston, User:William P Fuchs for their collaboration work on this assignment outside of class. In lab we reviewed the paper and figures and completed our presentation slides.
  • I would also like to acknowledge the help I received via email from User:Kam D. Dahlquist regarding uploading images and copyright issues for the outline section of this assignment
  • Although I received help on this assignment everything completed was my own work and was not copied from anyone else

Zachary T. Goldstein 02:02, 25 October 2016 (EDT)Zachary T. Goldstein



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