Week 8 Individual Journal William P Fuchs: Difference between revisions

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**Paper seeks to abridge this complication by utilizing computer assisted modeling-reconstruction programs.
**Paper seeks to abridge this complication by utilizing computer assisted modeling-reconstruction programs.
** The V3 region was analyzed and the amino acids around the inflexible regions were identified and the structure-function analysis was performed in order to provide insight in regards to the anti-AIDS research commitment.
** The V3 region was analyzed and the amino acids around the inflexible regions were identified and the structure-function analysis was performed in order to provide insight in regards to the anti-AIDS research commitment.
*Several sequential steps were initiated
*Several sequential steps were initiated:
**The following steps were conducted through the usual paradigm of analysis when discussing the general quality and characteristics of proteins.
**The following steps were conducted through the usual paradigm of analysis when discussing the general quality and characteristics of proteins.
#*comparative modeling and simulated annealing was run
***comparative modeling and simulated annealing was run.
##*from which the collection of  the low-energy structures were generated to find a consensus amino acid sequence for the HIV-1 subtype A V3 loop.
***from which the collection of  the low-energy structures were generated to find a consensus amino acid sequence for the HIV-1 subtype A V3 loop.
***the building blocks of the secondary V3 structures of the built conformations were characterized and recorded.
***common structural motifs in the HIV-1 V3 loops were located.
***after registering the intrinsic features of the SA-V3 loop,a molecular dynamics (MD) trajectory was derived from its static 3D structure. Then finding the structurally flexible and rigid V3 sections and comparing those findings with the prior obtained structures of the loop.
***then to measure the masking effect that can occur with the interaction of the SA-V3 loop.
***Other pertinent inner atomic interactions were evaluated to holistically research the loop structure.
*From the analysis and data on molecular docking, it would seem that synthetic molecules copying the amino acid sequences of the (FKBP and CycA) peptides is pheasable in making V3-based anti-HIV-1 drug projects a reality.


===Methods===
===Methods===

Revision as of 22:42, 23 October 2016

10 Previously Unknown Biological Terms

  1. glycosylated
  2. algorithm
  3. chemokine
  4. immunochemical
  5. crystallography
  6. simulated annealing
  7. dihedral angles
  8. proteoglycans
  9. tropism
  10. glycosyltransferase

Outline of Andrianov & Anishchenko's Paper

Link to full article:PDF of paper

Introduction

  • The virions enter the host cells though sequential interactions the CD4 cell surface receptors
  • After binding to the CD4 binding site, a 180 degree switch in the surface protein gp120 of the virus exposes the co-receptor binding site.
  • V3 loop of the glycoprotein gp120 is 35 residues long and highly variable
    • plays a central role in the virus biology in human invasion and immune system interaction.
    • is the head determinant for co-receptor binding.
    • HIV-1 V3 loop sequences are highly conserved.
  • Since the V3 region has a highly conserved nature it is a promising target for antiviral research.
    • Subsequently, V3 has become the focus of many developers of antiviral drugs.
  • Subtype A of HIV-1 is receives the short end of a disproportionate research preference to the HIV subtypes.
    • Paper seeks to abridge this complication by utilizing computer assisted modeling-reconstruction programs.
    • The V3 region was analyzed and the amino acids around the inflexible regions were identified and the structure-function analysis was performed in order to provide insight in regards to the anti-AIDS research commitment.
  • Several sequential steps were initiated:
    • The following steps were conducted through the usual paradigm of analysis when discussing the general quality and characteristics of proteins.
      • comparative modeling and simulated annealing was run.
      • from which the collection of the low-energy structures were generated to find a consensus amino acid sequence for the HIV-1 subtype A V3 loop.
      • the building blocks of the secondary V3 structures of the built conformations were characterized and recorded.
      • common structural motifs in the HIV-1 V3 loops were located.
      • after registering the intrinsic features of the SA-V3 loop,a molecular dynamics (MD) trajectory was derived from its static 3D structure. Then finding the structurally flexible and rigid V3 sections and comparing those findings with the prior obtained structures of the loop.
      • then to measure the masking effect that can occur with the interaction of the SA-V3 loop.
      • Other pertinent inner atomic interactions were evaluated to holistically research the loop structure.
  • From the analysis and data on molecular docking, it would seem that synthetic molecules copying the amino acid sequences of the (FKBP and CycA) peptides is pheasable in making V3-based anti-HIV-1 drug projects a reality.

Methods

Results and Discussion

Acknowledgements

References

  • Andrianov, A. M., & Anishchenko, I. V. (2009). Computational model of the HIV-1 subtype A V3 loop: Study on the conformational mobility for structure-based anti-AIDS drug design. Journal of Biomolecular Structure and Dynamics, 27(2), 179-193. http://dx.doi.org/10.1080/07391102.2009.10507308

Externals

Individual Journals

Class Journals

Assignments

Useful Links

  1. Bio Class Page
  2. BIOL368/F16:People
  3. Will Fuchs
  4. Link to LMU: http://www.lmu.edu/
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