Rabies virus 3d model

We greatly appreciate you choosing our 3D models and hope they will be of use. We look forward to continuously dealing with you. Rabies Virus. Use to navigate. Press esc to quit. Rabies Virus 3D model. This trimer model shows the number of interactions across two interfaces as well as details of the individual residue-residue interactions across these interfaces Figure 5. The interactions analysis in the 3D structure was obtained by a PDBsum server; for these hydrogen bonds and other nonbonded, disulfide bridges of CYS between two side chains or the formation of an amide bond —CO—NH— between side chains of Lys and a dicarboxylic aminoacid Glu or Asp were considered.

These stabilize the structure Figure 6. The stereochemical quality of the RABVG 3D structure was checked with a Ramachandran plot by analyzing the backbone dihedral angles residue by residue. The result showed that The overall model quality can be checked with ProsA -score that is used to check whether the input structure is within the range of scores typically found for native proteins of similar size [ 27 ].

The model reliability was further checked by ERRAT [ 45 ] that analyzes the statistics of nonbonded interactions between different atom types and plots the value of the error function versus position of a 9-residue sliding window as calculated by a comparison with statistics from highly refined structures. This suggests that the system reached structural stability and simulation integrity.

On the other hand, the residues we used in the root mean square fluctuations RMSF identify the regions responsible for the fluctuations during the MD simulations. The areas with higher fluctuations correspond to beta-loop-beta chains residues and turn regions. During the MD simulation, no structural uncoiling was observed. The regions with the most fluctuations have not been described as important areas to maintain the structural stability of the G protein trimer.

This does not generate significant changes within the main trimer binding regions. It maintained the trimer bound and conserved key interactions to maintain the stability of the structure. The interactions between residues, to , are directly linked to the structure of the prefusion and postfusion of Glycoprotein.

These interactions are important to maintain these structures. This is important for structural stability of the G protein trimer. It might be a good target for antiviral compounds because such modifications would change the helical conformation and be detrimental to the virus. The fluctuations that occurred during the molecular dynamics do not affect the stability of the structure of G protein trimer.

This is an open access article distributed under the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Article of the Year Award: Outstanding research contributions of , as selected by our Chief Editors.

Read the winning articles. Journal overview. Special Issues. Academic Editor: Serdar Kuyucak. Received 08 Dec Revised 21 Feb Accepted 06 Mar Published 24 Apr Material and Methods 2. Results 3. Table 1. Figure 1.

Figure 2. A transmembrane motif is revealed along with a amino acid signal peptide at the extracellular N-terminus. Figure 3. Domains of glycoprotein. The top lateral domain DI contains about 90 residues in two segments 1 to 17 and to It is made of two segments 36 to 50 and to and has the fold of a pH domain. Fusion DIV 51 to is inserted in a loop of the pH domain and is made of an extended sheet structure at the tip of which two loops are located that constitute the membrane-interacting motif of the G ectodomain.

Figure 4. Schematic diagram showing the interactions between the subunits. Figure 5. A model showing the number of interactions across the interfaces and the individual residue-residue interactions across the interfaces along with involved residues. These include interactions between A and B interface, interaction between A and C interface, and interaction between B and C.

Figure 6. Figure 7. Figure 8. On the error axis, two lines are drawn to indicate the confidence with which it is possible to reject regions that exceed that error value. For lower resolutions 2. Figure 9. Figure Chain C conformational chance during molecular dynamics. References G. View at: Google Scholar A. Albertini, R. Ruigrok, and D. Albertini, G.

Schoehn, W. Weissenhorn, and R. Rustici, L. Bracci, L. Lozzi et al. Gaudin, R. Ruigrok, C. Tuffereau, M.

Knossow, and A. Gaudin, S. Moreira, J. Blondel, A. Flamand, and C. Mousli, P. England, and C. Anilionis, W. Wunner, and P. Lentz, T. Burrage, A. Smith, and G. View Full Cart. Open Support Ticket. Close the Cart. Invalid Payment Information. Please complete the required fields. For help: Chat or Contact Support. Billing Address.

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