Archives

  • 2018-07
  • 2018-10
  • 2018-11
  • 2019-04
  • 2019-05
  • 2019-06
  • 2019-07
  • 2019-08
  • 2019-09
  • 2019-10
  • 2019-11
  • 2019-12
  • 2020-01
  • 2020-02
  • 2020-03
  • 2020-04
  • 2020-05
  • 2020-06
  • 2020-07
  • 2020-08
  • 2020-09
  • 2020-10
  • 2020-11
  • 2020-12
  • 2021-01
  • 2021-02
  • 2021-03
  • 2021-04
  • 2021-05
  • 2021-06
  • 2021-07
  • 2021-08
  • 2021-09
  • 2021-10
  • 2021-11
  • 2021-12
  • 2022-01
  • 2022-02
  • 2022-03
  • 2022-04
  • 2022-05
  • 2022-06
  • 2022-07
  • 2022-08
  • 2022-09
  • 2022-10
  • 2022-11
  • 2022-12
  • 2023-01
  • 2023-02
  • 2023-03
  • 2023-04
  • 2023-05
  • 2023-06
  • 2023-07
  • 2023-08
  • 2023-09
  • 2023-10
  • 2023-11
  • 2023-12
  • 2024-01
  • 2024-02
  • 2024-03
  • Fig lists the four critical assembly intermediates identifie

    2018-11-03

    Fig. 2 lists the four critical assembly intermediates identified in our simulations, which can be seen in the movies (Movies 1 to 5) compiled with snapshots of representative simulations of four structural models. Fig. 3 illustrates the assembly of a system comprised of 128 dimeric subunits based on 3J34.pdb. Representative trimer and hexamers are highlighted in Fig. 3A, C and D. The quantitative analysis of the assembly pathway of the system is shown in Fig. 7. Fig. 4 shows the variation of contact angles of neighboring subunits in 3J34.pdb between NTD–NTD, NTD–CTD, and CTD–CTD interfaces. Fig. 5 shows the rotation necessary to align the NTDs of the dimer at subsequent time points to t=0 along the trajectory of the 303ns all CM-272 MD simulations of a dimer based on chains A and f in 3J34.pdb. Fig. 6 shows the flexibility of the NTDs and CTDs in a dimeric HIV capsid protein measured by the angles to align the domains along the trajectory of the 303ns all atom MD simulations of a dimer based on chains A and f in 3J34.pdb (in A), compared to that measured by solution NMR (in B). Fig. 7 shows the quantitative analysis of the assembly pathway of a representative simulations (snapshots of the assembly shown in Fig. 3) with 128 dimeric subunits based on 3J34.pdb. Detailed view of the evolution of simulations based on different structural templates are shown by Movies 1–5, compiled with snapshots taken from respective simulations.
    Experimental design, materials and methods
    Acknowledgments The authors acknowledge help from Drs. Juan Perilla and Klaus Schulten at UIUC for the 303ns MD simulation of HIV capsid dimer. The authors appreciate suggestions and comments from Lalit Deshmukh and Dr. Robert Tycko at NIDDK, NIH, and assistance from Dr. John Stone at UIUC and Prof. Alexander Balaeff at UCF with VMD. This work is supported by AFOSR young investigator award, Grant number FA9550-13-1-0150.
    Specifications table
    Value of the data
    Data Nucleotide sequences of each transcript used to assemble the mitogenomes of three Ancistrus spp. fish described by Moreira et al. [6] are available in fasta format (supplemental material). Table 1 shows the number and the length of each of those mitochondrial transcripts, as well as the maximum number of supporting reads per individual nucleotide and the total sum of supporting reads for each transcript. The position of heteroplasmic sites is shown at Table 2, along with the read counts of each nucleotide, the gene category and the codon position of each heteroplasmy. Specifically for protein-coding genes, Table 3 shows the lengths of 5′UTR, 3′UTR, ORF and Poly-A tail. In addition, Table 3 also shows the initiation and the termination codon, as well as the number of Adenines added to complete the stop codons, if needed.
    Experimental design, materials and methods Fish sampling, RNA extraction, Illumina library preparation and sequencing, raw reads processing and transcriprtome assemble are described elsewhere [6]. Each transcriptome was subjected to a BLASTN against the complete mitogenome of the closest related species, whose mitogenome is publically available, Pterygoplichthys disjunctivus (GI: 339506171) [7]. The transcripts aligned to the reference mitogenome were used for the mitogenomes assembly. The selected transcripts were edited according to the information of strand orientation given by the BLASTN result, and aligned by SeaView using the built-in CLUSTAL alignment algorithm and the reference mitogenome [2]. A CONTIG sequence was generated using the sequence information of just the transcripts of each individual fish. The sequence of the CONTIG was then manually checked for inconsistencies and gaps. The mitogenomes were annotated using the web-based services MitoFish and MITOS [1,3] and features in protein-coding genes were analyzed according to Temperley et al. [9]. In order to estimate the support of each base in the mitogenomes, Bowtie v. 1.0.0 was used to align the reads of each fish on its own assembled mitogenome, and this mapping was viewed using the Integrated Genome Viewer (IGV) or the Tablet [10,4,5,8]. Heteroplasmic sites were detected using IGV, setting the software to show positions in which the frequency of the second most frequent base was equal to or higher than 10% and the total reads number were higher than 100.