Structure of trimeric HIV-1 envelope glycoproteins.
Structure of trimeric HIV-1 envelope glycoproteins.
复制标题
三聚体 HIV-1 包膜糖蛋白的结构。
DOI：
10.1073/pnas.1313802110
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发表时间：
2013
影响因子：
11.1
通讯作者：
Subramaniam,Sriram
中科院分区：
文献类型：
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作者：
Subramaniam,Sriram
Mao et al.(1) published a paper describing a 3D structure of uncleaved, trimeric HIV-1 envelope glycoprotein (Env) at∼ 6-Å resolution, following a similar paper last year on the same structure at∼ 11-Å resolution (2). Examination of these two papers leads me to doubt that the structures presented are results of a reliable cryo-electron microscopic analysis of purified HIV-1 Env trimers. An underlying assumption in structure determination by cryo-electron microscopy is that there is demonstrable evidence that the micrographs contain images of the relevant proteins, although their mere existence in no way guarantees that a structure at 6 Å, or even at 11 Å, can be obtained. The raw electron micrographs presented by Mao et al.(1, 2) do not provide convincing evidence for the presence of molecular images of HIV-1 Env trimers [compare fig. 1A from Mao et al.(1) with fig. 1B from Harris et al.(3), where trimers are clearly visible in the images]. I am therefore concerned that the authors have fallen into the well-known reference-bias trap in image processing by recovering what looks like a real structure starting from images of random noise. Support for this concern comes from inspection of the density maps deposited in the Electron Microscopy Data Bank (EMD-5447 and EMD-5418 from refs. 1 and 2, respectively). EMD-5418 closely matches a related map determined earlier using cryo-electron tomography (ref. 4, EMD-5019) that may have been used as a mask during image processing (Fig. 1 C–F). Further, the claim that the structure of the uncleaved trimeric HIV-1 Env as presented in the work of Mao et al.(1, 2) is in agreement with the structure of native, cleaved trimeric HIV-1 Env presented in Liu et al.(4) is incorrect. EMD-5019 represents only the ectodomain of the Env trimer; it does not include the transmembrane region, which was deposited separately (EMD-5022). Assignment of the end regions of the maps presented by Mao et al. to the gp41 transmembrane helices (1, 2)(Fig. 1 D and G) thus contradicts the earlier cryo-electron tomography results (4). Quantitative comparison of the maps deposited by Mao et al. at resolutions of∼ 11 (2) and∼ 6 Å (1) shows that the Fourier shell coefficient falls to zero at∼ 11 Å (Fig. 2A). If the latter map was derived from the former, as the authors write, the correlation at∼ 11 Å would be nearly 100% and not zero. Further, filtering the 6-Å map to a resolution of 11 Å yields a map that is markedly different from EMD-5418 (Fig. 2A, Inset). The most ordered regions of EMD-5447 are the gp41 transmembrane helices, which stand out clearly against the background, and the V4 loop, which is disordered in crystal structures of monomeric gp120 (5)(Fig. 2 B–D). A plausible explanation for these surprising map features is that the authors used a molecular model to select particles from their micrographs; in this case, the refinement process would be circular, resulting in a final map that recapitulates the starting template. It will not be possible to determine the validity of the results of Mao et al.(1, 2) unless they make publicly available their original micrographs, list of locations where particles were selected, and a complete description of the protocols used for image processing.
