The structure of eukaryotic and prokaryotic complex I

Abstract

The structures of the NADH dehydrogenases from Bos taurus and Aquifex aeolicus have been determined by 3D electron microscopy, and have been analyzed in comparison with the previously determined structure of Complex I from Yarrowia lipolytica. The results show a clearly preserved domain structure in the peripheral arm of complex I, which is similar in the bacterial and eukaryotic complex. The membrane arms of both eukaryotic complexes show a similar shape but also significant differences in distinctive domains. One of the major protuberances observed in Y. lipolytica complex I appears missing in the bovine complex, while a protuberance not found in Y. lipolytica connects in bovine complex I a domain of the peripheral arm to the membrane arm. The structural similarities of the peripheral arm agree with the common functional principle of all complex Is. The differences seen in the membrane arm may indicate differences in the regulatory mechanism of the enzyme in different species.

Figure 1

Structure of Y. lipolytica complex I (Radermacher et al., 2006). The matrix arm clearly shows six domains (numbered 1 – 6). The membrane arm shows a distal membrane arm protuberance (DMP) and a central membrane arm protuberance (CMP). The surface facing the inter-membrane space shows two major protuberances IP1 and IP2.

Figure 2

Hypothetical model of a conformationally driven proton pumping mechanism. As observed occasionally in 2D averages of Y. lipolytica complex I domain 5 may be connected via a tether to the membrane protuberances, facilitating the transfer of conformational changes in the matrix arm to locations close to the proton pumping subunits in the membrane arm. Alternatively the conformational changes may be transferred through a more internal conformational coupling mechanism. (from http://physiology.med.uvm.edu/radermacher/, with permission)

Figure 3

Parts of a tilt pair of bovine complex I. a) tilt image, b) 0°-image. Dashed line tilt-axis. Arrows indicate typical particle pairs that were selected from the micrographs. Scale bar 100nm.

Figure 4

a) Results of correspondence analysis of the 0°-images of bovine complex I. Shown is the visual representation of the map 1 vs. 2. Each image represents an average image of all single images whose coordinates fall within the same square. b) The five class averages (numbered 1–5) obtained after moving center classification followed by hierarchical ascendant classification. Scale bar 10 nm

Figure 5

3D volumes of the five classes shown in figure 4b (same numbering). a) All five volumes without any relative alignment. b) Top views of the five reconstructions, aligned visually. The main difference between classes 1,2 and 5 is orientation. Scale bar 10 nm

Figure 6

The 3D structure of bovine complex I. The same domains as found in the Y. lipolytica complex I appear in bovine complex I (numbered 1–6). The distal membrane protuberance is present (DMP). A second, proximal membrane protuberance (PMP) appears in a location different from CMP found in Y. lipolytica complex I, and connects to domain 6. Protrusion DMP is larger than in the Y. lipolytica enzyme and may include CMP. The intermembrane face of bovine complex I shows three protuberances IP1 – IP3. IP1 and IP3 in bovine complex I may correspond to the single IP1 in Y.lipolytica complex I. Scale bar 10 nm.

Figure 7

Parts of a tilt pair of complex I from A. aeolicus. a) tilt image, b) 0°-image. Dashed line tilt-axis. The 0°-image most clearly shows the high heterogeneity of the sample and the frequent overlap of particles. Arrows indicate typical particle pairs that were selected from the micrographs. Scale bar 100nm.

Figure 8

a) Results of correspondence analysis of the 0°-images of complex I from A. aeolicus. Shown is the visual representation of the map 1 vs. 2. b) The three class averages obtained after moving center classification followed by hierarchical ascendant classification (numbered 1–3). c) Volumes reconstructed from the tilt images belonging to the same three classes. Volumes in their original relative orientations. No volume alignment has been applied. Scale bars 10 nm.

Figure 9

Sub-classification of classes 1 and 3 shown in Fig. 6 of the image data of A. aeolicus. a) b) Class 1 divided into seven subclasses. a) Class averages numbered 1.1 – 1.7, b) 3D reconstructions for classes 1.1 – 1.7. c, d, Class 3 was divided into 11 subclasses. c) Class averages numbered 3.1–3.11, d) 3D reconstructions for classes 1.1 – 1.11. Scale bars 10 nm.

Figure 10

3D reconstruction of complex I from A. aeolicus calculated from the merged data set from classes 3.8, 3.10 and 3.11. Clearly recognizable are domains 1, 2 and 5. Scale bar 10 nm.

Figure 11

Comparison of the three structures of complex I from the yeast Y. lipolytica, the mammalian bovine complex I and the bacterial complex I from A. aeolicus. Resolutions from left to right: 24Å, 27Å, 45Å. Scale bar 10 nm.