Matthew K. Oki Individual Journal 8
- 1 Preparation for Week 9 Journal Club
Preparation for Week 9 Journal Club
- "One of a group of compounds consisting of a protein combined with a carbohydrate (such as galactose or mannose). Examples of glycoproteins are certain enzymes, hormones, and antigens."
- Simulated Annealing Algorithm
- "A technique used in data mining to select an optimal set of data from a large space of solutions. The term comes from the fact that the techniques uses a process similar to that found when metals are cooled slowly."
- Chemokine co-receptors
- "Any one of a group of small proteins that guide leucocytes to sites of infection and are vital for immune function. They fall into two main classes, CC chemokines and CXC chemokines; receptors (denoted R) are named after the class that bind to them, and subtypes of each class are indicated by numbers (e.g. CCR5)."
- "any specific immunological reagent that consists of or incorporates an antigen or an antibody, especially one of commerce."
- X-ray crystallography
- "The study of the geometric forms of crystals by X‐ray diffraction."
- "Lasting only for a short period of time."
- "An angle formed by the intersection of two planes (e.g. two faces of a polyhedron). The dihedral angle is the angle formed by taking a point on the line of intersection and drawing two lines from this point, one in each plane, perpendicular to the line of intersection."
- "Capable of stimulating an immune response."
- "An ordering of the internal character set, used in alphabetic and alphanumeric sorting."
- "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."
- HIV-1 enters the host cell through interaction with CD4 cell surface receptors and a chemokine co-receptor.
- The V3 loop is a highly variable portion of HIV-1 that is the target for antiviral drugs.
- The variability prevents antibodies from affecting any other isolates.
- However, some of the amino acid positions in the N-and C- terminals are conserved.
- They are most likely conserved to preserve the conformational status of the virus
- The 3D structure of HIV-1 must be found to implement drugs that can inflict the conserved portion of the virus.
- HIV-1 Subtype B dominates North and South American and is given preference in research, but computer-made structures are helping close the gap for subtype A, which prevails in Central Africa and Eastern Europe.
- 5 major steps were completed in this study:
- The low-energy confirmation for the V3 loop of HIV-1 subtype A was generated
- The secondary structures of V3 were characterized in the built conformations
- NMR spectroscopy and X-rays were used to reveal the motif structures of the V3 loop
- The molecular dynamics trajectory was found to investigate the conformational features in more depth
- Finally, molecular docking was used to see if the V3 loop kept in touch with the ligands
- Modeling of 3D V3 Structures
- Comparative modeling methods were used on the structures found from NMR spectroscopy and X-ray studies
- The MODELLAR package was used in comparative modeling of 100 models for each template.
- The subsets with the 10 best models were selected for energy optimization and final refinement
- The AMBER and TINKER software were used to find energy optimizations
- Identification of Secondary V3 Structures
- The phi and psi bond values of each amino acid were derived from the simulated models
- Classical and non-standard B-turns were found by using classifications created by previous authors.
- Comparison of 3D V3 Structures
- Root-mean-square deviations were calculated for the entire V3 structure and the individual fragments of 4 to 9 residues
- Molecular Dynamics Computations
- GROMACS software was used for molecular dynamics computations
- Molecular Docking Simulations
- These simulations were presented in the Hex 4.5 program in order to display possible docking areas for pairs of protein and DNA
- Figure 1: Displayed the 3D figures for 3 segments of the V3 region of HIV-1. The segments of note include residues 3-7, 15-19, 28-32. The segments were analyzed for cRMSD and aRMSD, which represent the structural similarity/stability for each segment.
- Figure 2: Displayed the most energy-optimized structure found in computer software. This structure shows different secondary structures such as B-turns and alpha helices.
- Figure 3: Shows a primary sequence of amino acids with protruding secondary structures. There are visibly more secondary structures at the ends and in the middle of the V3 loop. This middle area, where the helix is located, is called the immunogenic tip.
- Figure 4: Displays the variability of each segment as cRMSD values. The higher the cRMSD value, the more variability there is. So, segment 1 had the highest variability, while segment 2 had the least.
- Figure 5: Gives cRMSD means over time for 11 different V3 segments. The area that is pinched represents residues of very low flexibility. The valley in the graph shows the immunogenic tip.
- Figure 6: Gives the aRMSD values for the phi and psi bond angles. These are the bond angles in the sequence that can be rotated around. The valley in this figure also represents the immunogenic tip.
- Figure 7: Gives a computer-generated model of the V3 loop bound to CycA and FKBP. This shows that the V3 loop not only binds at the immunogenic tip, but also at another binding site.
- The most probable 3D structure was derived for subtype A HIV-1 with the help of previous studies’ data and energy conservation.
- Subtype A was chosen because so much more research has been done on subtype B
- The N- and C- terminals and the immunogenic tip were found to be very rigid with few conformational changes.
- This is big news for a virus that is giving medicine trouble with its high variability.
- The regions of this V3 gene can be the key to solving the puzzle of HIV-1
- In terms of future studies, they can pursue studies on the other subtypes of HIV-1.
- What is the main result (message) presented in this paper?
- The main message of this paper is that there is significantly more rigidity in the V3 loop than in the rest of HIV-1. This rigidity is due to the fact that it must keep its pinched state to keep the immunogenic tip in its confirmation. Without these rigid segments, the immunogenic tip wouldn't be held in a loop.
- What is the importance or significance of this work?
- This is a possible point of attack for medicine. A major issue with trying to combat HIV-1 is the high variance it displays. An exception to this is the immunogenic tip in the V3 loop region. However, they didn't go into great detail on how exactly the antibodies would attack these rigid areas.
- What were the limitations in previous studies that led them to perform this work?
- The other studies had the issue of sample size and only looking at subtype B. This group wanted to take a look at another subtype of HIV-1 and provide some much needed data.
- What were the methods used in the study?
- Described above
- Briefly state the result shown in each of the figures and tables.
- Described above
- How do the results of this study compare to the results of previous studies.
- Previous models were confirmed with this research, given that there is not much previous research to begin with.
- I would like to thank my partners, Mia Huddleston, Zachary T. Goldstein, and William P. Fuchs, for the assistance on this weeks project both in the understanding of our paper in class and completion of the powerpoint outside of class
- I would also like to thank Kam D. Dahlquist, Ph.D. for providing the instructions and information for this assignment both in class and on this document: BIOL368/F16:Week 8.
- Even though I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
- Matthew K. Oki 17:44, 19 October 2016 (EDT):
- BIOL368/F16:Week 8
- 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. DOI: 10.1080/07391102.2009.10507308
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