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5.6: Structure of Electron Carriers - Biology

5.6: Structure of Electron Carriers - Biology


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Though they have been mentioned frequently in the earlier parts of this chapter, the structures of the electron transport chain participants, and particularly of the moieties that temporarily hold extra electrons, have not been addressed. The major players are the flavin mononucleotide (FMN) that plays a role in complex I, ubiquinone (Coenzyme Q), the lipid-soluble electron carrier, the heme groups of the cytochromes, and iron-sulfur clusters, found in complexes I, II, and III.

Flavin mononucleotide (FMN) or flavin adenine dinucleotide (FAD), are pictured in Figure (PageIndex{11}). Note the triple-ring structure and the three possible oxidation states. All three states are stable - the semiquinone state is not merely a transient form. This stability allows the conversion from carriers that can only handle one electron to carriers that can handle two electrons, and vice versa. The same holds true for ubiquinone - stable as ubiquinone (fully oxidized), semiubiquinone (radical state), and ubiquinol (fully reduced). Alternative nomenclature for these molecules is Coenzyme Q, CoQH+, and CoQH2. Note the aromaticity gained by ubiquinone when it is reduced. This enhances its stability and its suitability as a receiver of electrons from NADH.

Heme groups (Figure (PageIndex{12})) are considerably larger, encompassing a porphyrin ring with an iron ion held in its center. This iron ion alternates between ferric (Fe3+) and ferrous (Fe2+) states as the heme group is oxidized and reduced, respectively. In the case of complex IV, the iron ion can form a complex with O2, which can then receive the electrons being held by the ring structure. This large structure is particularly important because it needs to be able to transfer a total of 4 electrons to reduce O2 to 2 H2O.

Finally, Fe-S clusters (Figure (PageIndex{12})) can also act as electron carrying moieties. Like in the heme group, the iron atom can readily switch between the ferric and ferrous states.


Photosynthesis occurs inside chloroplasts. Chloroplasts contain chlorophyll, a green pigment found inside the thylakoid membranes. These chlorophyll molecules are arranged in groups called photosystems. There are two types of photosystems, Photosystem II and Photosystem I. When a chlorophyll molecule absorbs light, the energy from this light raises an electron within the chlorophyll molecule to a higher energy state. The chlorophyll molecule is then said to be photoactivated. Excited electron anywhere within the photosystem are then passed on from one chlorophyll molecule to the next until they reach a special chlorophyll molecule at the reaction centre of the photosystem. This special chlorophyll molecule then passes on the excited electron to a chain of electron carriers.

The light-dependent reactions starts within Photosystem II. When the excited electron reaches the special chlorophyll molecule at the reaction centre of Photosystem II it is passed on to the chain of electron carriers. This chain of electron carriers is found within the thylakoid membrane. As this excited electron passes from one carrier to the next it releases energy. This energy is used to pump protons (hydrogen ions) across the thylakoid membrane and into the space within the thylakoids. This forms a proton gradient. The protons can travel back across the membrane, down the concentration gradient, however to do so they must pass through ATP synthase. ATP synthase is located in the thylakoid membrane and it uses the energy released from the movement of protons down their concentration gradient to synthesise ATP from ADP and inorganic phosphate. The synthesis of ATP in this manner is called non-cyclic photophosphorylation (uses the energy of excited electrons from photosystem II) .

The electrons from the chain of electron carriers are then accepted by Photosystem I. These electrons replace electrons previously lost from Photosystem I. Photosystem I then absorbs light and becomes photoactivated. The electrons become excited again as they are raised to a higher energy state. These excited electrons then pass along a short chain of electron carriers and are eventually used to reduce NADP + in the stroma. NADP + accepts two excited electrons from the chain of carriers and one H + ion from the stroma to form NADPH.

If the light intensity is not a limiting factor, there will usually be a shortage of NADP + as NADPH accumulates within the stroma (see light independent reaction). NADP + is needed for the normal flow of electrons in the thylakoid membranes as it is the final electron acceptor. If NADP + is not available then the normal flow of electrons is inhibited. However, there is an alternative pathway for ATP production in this case and it is called cyclic photophosphorylation. It begins with Photosystem I absorbing light and becoming photoactivated. The excited electrons from Photosystem I are then passed on to a chain of electron carriers between Photosystem I and II. These electrons travel along the chain of carriers back to Photosystem I and as they do so they cause the pumping of protons across the thylakoid membrane and therefore create a proton gradient. As explained previously, the protons move back across the thylakoid membrane through ATP synthase and as they do so, ATP is produced. Therefore, ATP can be produced even when there is a shortage of NADP + .

In addition to producing NADPH, the light dependent reactions also produce oxygen as a waste product. When the special chlorophyll molecule at the reaction centre passes on the electrons to the chain of electron carriers, it becomes positively charged. With the aid of an enzyme at the reaction centre, water molecules within the thylakoid space are split. Oxygen and H + ions are formed as a result and the electrons from the splitting of these water molecules are given to chlorophyll. The oxygen is then excreted as a waste product. This splitting of water molecules is called photolysis as it only occurs in the presence of light.


Complex I

To start, two electrons are carried to the first complex aboard NADH. This complex, labeled I, is composed of flavin mononucleotide (FMN) and an iron-sulfur (Fe-S)-containing protein. FMN, which is derived from vitamin B2, also called riboflavin, is one of several prosthetic groups or co-factors in the electron transport chain. A prosthetic group is a non-protein molecule required for the activity of a protein. Prosthetic groups are organic or inorganic, non-peptide molecules bound to a protein that facilitate its function prosthetic groups include co-enzymes, which are the prosthetic groups of enzymes. The enzyme in complex I is NADH dehydrogenase and is a very large protein, containing 45 amino acid chains. Complex I can pump four hydrogen ions across the membrane from the matrix into the intermembrane space, and it is in this way that the hydrogen ion gradient is established and maintained between the two compartments separated by the inner mitochondrial membrane.


Electron Transport Chain

L. Aerts , V.A. Morais , in Parkinson's Disease , 2017

Abstract

The protein complexes that comprise the electron transport chain (ETC) fuel the production of ATP, the universal biochemical energy currency. Defects in ETC function have widespread consequences and are linked to neurodegenerative diseases, including Parkinson’s disease (PD). Defects in NADH:ubiquinone oxidoreductase, the first complex in the ETC, have been found in both sporadic and familial cases of PD. Here, we list the evidence for the role of ETC dysfunction in the pathogenesis of PD and highlight how therapeutic approaches aimed at stimulating electron transport could be beneficial for both familial and sporadic cases of PD.


Flavin Adenine Dinucleotide

Flavin adenine dinucleotide, or FAD, consists of riboflavin attached to an adenosine diphosphate molecule. It is capable of accepting and donating one or two electrons. It is often bound firmly to an enzyme site, so not very much free FAD exists in a cell. Some FAD is formed during the citric acid cycle of cellular respiration. One function of FAD is to donate electrons to oxidative phosphorylation, where the electrons from the reduced form of FAD are transferred to create adenosine triphosphate (ATP), the energy currency of the cell. This process happens in the mitochondria of the cell.


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The First Steps of Cellular Respiration

The first step of cellular respiration is glycolysis. Glycolysis occurs in the cytoplasm and involves the splitting of one molecule of glucose into two molecules of the chemical compound pyruvate. In all, two molecules of ATP and two molecules of NADH (high energy, electron carrying molecule) are generated.

The second step, called the citric acid cycle or Krebs cycle, is when pyruvate is transported across the outer and inner mitochondrial membranes into the mitochondrial matrix. Pyruvate is further oxidized in the Krebs cycle producing two more molecules of ATP, as well as NADH and FADH 2 molecules. Electrons from NADH and FADH2 are transferred to the third step of cellular respiration, the electron transport chain.


Table 6.1 - Reduction potentials of FMN couples.

Abbreviations: Q, quinone SQ, semiquinone HQ, hydroquinone.
E°Q/SQ E°SQ/HQ
Free FMN -238 mV -172 mV
C.M.P. flavodoxin -92 mV -399 mV

The blue copper proteins are characterized by intense S(Cys) &rarr Cu chargetransfer absorption near 600 nm, an axial EPR spectrum displaying an unusually small hyperfine coupling constant, and a relatively high reduction potential. 4,8-10 With few exceptions (e.g., photosynthetic organisms), their precise roles in bacterial and plant physiology remain obscure. X-ray structures of several blue copper proteins indicate that the geometry of the copper site is approximately trigonal planar, as illustrated by the Alcaligenes denitrificans azurin structure (Figure 6.5). 11,12 In all these proteins, three ligands (one Cys, two His) bind tightly to the copper in a trigonal arrangement. Differences in interactions between the copper center and the axially disposed ligands may significantly contribute to variations in reduction potential that are observed 12 for the blue copper electron transferases. For example, E°' = 276 mV for A. denitrificans azurin, whereas that of P. vulgaris plastocyanin is 360 mV. In A. denitrificans azurin, the Cu-S(Met) bond is 0.2 Å longer than in poplar plastocyanin, and there is a carbonyl oxygen 3.1 Å from the copper center, compared with 3.8 Å in plastocyanin. These differences in bond lengths are expected to stabilize Cu ll in azurin to a greater extent than in plastocyanin, and result in a lower E°' value for azurin.

Figure 6.5 - Structure of the blue copper center in azurin. 11

The iron-sulfur proteins play important roles 13,14 as electron carriers in virtually all living organisms, and participate in plant photosynthesis, nitrogen fixation, steroid metabolism, and oxidative phosphorylation, as well as many other processes (Chapter 7). The optical spectra of all iron-sulfur proteins are very broad and almost featureless, due to numerous overlapping charge-transfer transitions that impart red-brown-black colors to these proteins. On the other hand, the EPR spectra of iron-sulfur clusters are quite distinctive, and they are of great value in the study of the redox chemistry of these proteins.

The simplest iron-sulfur proteins, known as rubredoxins, are primarily found in anaerobic bacteria, where their function is unknown. Rubredoxins are small proteins (6 kDa) and contain iron ligated to four Cys sulfurs in a distorted tetrahedral arrangement. The E°' value for the Fe III / II couple in water is 770 mV that of C. pasteurianum rubredoxin is -57 mV. The reduction potentials of iron-sulfur proteins are typically quite negative, indicating a stabilization of the oxidized form of the redox couple as a result of negatively charged sulfur ligands.

The [2Fe-2S] ferredoxins (10-20 kDa) are found in plant chloroplasts and mammalian tissue. The structure of Spirulina platensis ferredoxin 15 confirmed earlier suggestions, based on EPR and Mössbauer studies, that the iron atoms are present in a spin-coupled [2Fe-2S] cluster structure. One-electron reduction (E°'

-420 mV) of the protein results in a mixed-valence dimer (Equation 6.3):

[Fd_ qquad qquad qquad Fd_]

[2Fe(III) qquad qquad Fe(II) + Fe(III)]

The additional electron in Fdred is associated with only one of the iron sites, resulting in a so-called trapped-valence structure. 16 The [Fe2S2(SR)4] 4- cluster oxidation state, containing two ferrous ions, can be produced in vitro when strong reductants are used.

Four-iron clusters [4Fe-4S] are found in many strains of bacteria. In most of these bacterial iron-sulfur proteins, also termed ferredoxins, two such clusters are present in the protein. These proteins have reduction potentials in the -400 mV range and are rather small (6-10 kDa). Each of the clusters contains four iron centers and four sulfides at alternate comers of a distorted cube. Each iron is coordinated to three sulfides and one cysteine thiolate. The irons are strongly exchange-coupled, and the [4Fe-4S] cluster in bacterial ferredoxins is paramagnetic when reduced by one electron. The so-called "high-potential ironsulfur proteins" (HiPIPs) are found in photosynthetic bacteria, and exhibit anomalously high (

350 mV) reduction potentials. The C. vinosum HiPIP (10 kDa) structure demonstrates that HiPIPs are distinct from the [4Fe-4S] ferredoxins, and that the reduced HiPIP cluster structure is significantly distorted, as is also observed for the structure of the oxidized P. aerogenes ferredoxin. In addition, oxidized HiPIP is paramagnetic, whereas the reduced protein is EPR-silent.

This bewildering set of experimental observations can be rationalized in terms of a "three-state" hypothesis (i.e., [4Fe-4S(SR)4] n- clusters exist in three physiological oxidation states). 17 This hypothesis nicely explains the differences in magnetic behavior and redox properties observed for these iron-sulfur proteins (Equation 6.4):

[HiPIP_ qquad qquad qquad HiPIP_ qquad qquad qquad Ferredoxin_]

The bacterial ferredoxins and HiPIPs all possess tetracubane clusters containing thiolate ligands, yet the former utilize the -2/-3 cluster redox couple, whereas the latter utilize the -1/-2 cluster redox couple.

The protein environment thus exerts a powerful influence over the cluster reduction potentials. This observation applies to all classes of electron transferases&mdashthe factors that are critical determinants of cofactor reduction potentials are poorly understood at present but are thought 18 to include the low dielectric constants of protein interiors (

78 for H2O), electrostatic effects due to nearby charged amino-acid residues, hydrogen bonding, and geometric constraints imposed by the protein.

As a class, the cytochromes 19-22 are the most thoroughly characterized of the electron transferases. By definition, a cytochrome contains one or more heme cofactors. These proteins were among the first to be identified in cellular extracts because of their distinctive optical properties, particularly an intense absorption in the 410-430 nm region (called the Soret band). Cytochromes are typically classified on the basis of heme type. Figure 6.6 displays the three most commonly encountered types of heme: heme a possesses a long phytyl "tail" and is found in cytochrome c oxidase heme b is found in b-type cytochromes and globins heme c is covalently bound to c-type cytochromes via two thioether linkages. Cytochrome nomenclature presents a real challenge! Some cytochromes are designated according to the historical order of discovery, e.g., cytochrome c2 in bacterial photosynthesis. Others are designated according to the (lambda_)of the (alpha) band in the absorption spectrum of the reduced protein (e.g., cytochrome c551).

Figure 6.6 - Structures of hemes a, b, and c.

Cytochromes c are widespread in nature. Ambler 23 divided these electron carriers into three classes on structural grounds. The Class I cytochromes c contain axial His and Met ligands, with the heme located near the N-terrninus of the protein. These proteins are globular, as indicated by the ribbon drawing of tuna cytochrome c (Figure 6.7). X-ray structures of Class I cytochromes c from a variety of eukaryotes and prokaryotes clearly show an evolutionarily conserved "cytochrome fold," with the edge of the heme solvent-exposed. The reduction potentials of these cytochromes are quite positive (200 to 320 mV). Mammalian cytochrome c, because of its distinctive role in the mitochondrial electron-transfer chain, will be discussed later.

Figure 6. - Structure of tuna cytochrome c.

-100 mV) are found in photosynthetic bacteria, where they serve an unknown function. Unlike their Class I cousins, these c-type cytochromes are high-spin: the iron is five-coordinate, with an axial His ligand. These proteins, generally referred to as cytochromes c' , are four-(alpha)-helix bundles (Figure 6.8). The vacant axial coordination site is buried in the protein interior.

Figure 6.8 - Structure of cytochrome c'.

Finally, Class III cytochromes c, also called cytochromes c3, contain four hemes, each ligated by two axial histidines. These proteins are found in a restricted class of sulfate-reducing bacteria and may be associated with the cytoplasmic membrane. The low molecular weights of cytochromes c3 (

14. 7 kDa) require that the four hemes be much more exposed to the solvent than the hemes of other cytochromes (see Figure 6.9), which may be in part responsible for their unusually negative (-200 to -350 mV) reduction potentials. These proteins possess many aromatic residues and short heme-heme distances, two properties that could be responsible for their anomalously large solid-state electrical conductivity. 24


Contents

Subunits Edit

Mitochondrial and many bacterial SQRs are composed of four structurally different subunits: two hydrophilic and two hydrophobic. The first two subunits, a flavoprotein (SdhA) and an iron-sulfur protein (SdhB), form a hydrophilic head where enzymatic activity of the complex takes place. SdhA contains a covalently attached flavin adenine dinucleotide (FAD) cofactor and the succinate binding site and SdhB contains three iron-sulfur clusters: [2Fe-2S], [4Fe-4S], and [3Fe-4S]. The second two subunits are hydrophobic membrane anchor subunits, SdhC and SdhD. Human mitochondria contain two distinct isoforms of SdhA (Fp subunits type I and type II), these isoforms are also found in Ascaris suum and Caenorhabditis elegans. [3] The subunits form a membrane-bound cytochrome b complex with six transmembrane helices containing one heme b group and a ubiquinone-binding site. Two phospholipid molecules, one cardiolipin and one phosphatidylethanolamine, are also found in the SdhC and SdhD subunits (not shown in the image). They serve to occupy the hydrophobic space below the heme b. These subunits are displayed in the attached image. SdhA is green, SdhB is teal, SdhC is fuchsia, and SdhD is yellow. Around SdhC and SdhD is a phospholipid membrane with the intermembrane space at the top of the image. [4]

Table of subunit composition [5] Edit

No. Subunit name Human protein Protein description from UniProt Pfam family with Human protein
1 SdhA SDHA_HUMAN Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial Pfam PF00890, Pfam PF02910
2 SdhB SDHB_HUMAN Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial Pfam PF13085, Pfam PF13183
3 SdhC C560_HUMAN Succinate dehydrogenase cytochrome b560 subunit, mitochondrial Pfam PF01127
4 SdhD DHSD_HUMAN Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial Pfam PF05328

Ubiquinone binding site Edit

Two distinctive ubiquinone binding sites can be recognized on mammalian SDH – matrix-proximal QP and matrix-distal QD. Ubiquinone binding site Qp, which shows higher affinity to ubiquinone, is located in a gap composed of SdhB, SdhC, and SdhD. Ubiquinone is stabilized by the side chains of His207 of subunit B, Ser27 and Arg31 of subunit C, and Tyr83 of subunit D. The quinone ring is surrounded by Ile28 of subunit C and Pro160 of subunit B. These residues, along with Il209, Trp163, and Trp164 of subunit B, and Ser27 (C atom) of subunit C, form the hydrophobic environment of the quinone-binding pocket Qp. [6] In contrast, ubiquinone binding site QD, which lies closer to inter-membrane space, is composed of SdhD only and has lower affinity to ubiquinone. [7]

Succinate binding site Edit

SdhA provides the binding site for the oxidation of succinate. The side chains Thr254, His354, and Arg399 of subunit A stabilize the molecule while FAD oxidizes and carries the electrons to the first of the iron-sulfur clusters, [2Fe-2S]. [8] This can be seen in image 5.

Redox centers Edit

The succinate-binding site and ubiquinone-binding site are connected by a chain of redox centers including FAD and the iron-sulfur clusters. This chain extends over 40 Å through the enzyme monomer. All edge-to-edge distances between the centers are less than the suggested 14 Å limit for physiological electron transfer. [4] This electron transfer is demonstrated in image 8.

Subunit E Edit

In molecular biology, the protein domain named Sdh5 is also named SdhE which stands for succinate dehydrogenase protein E. In the past, it has also been named YgfY and DUF339. [9] Another name for SdhE is succinate dehydrogenase assembly factor 2 (Sdhaf2). [10] This protein belongs to a group of highly conserved small proteins found in both eukaryotes and prokaryotes, including NMA1147 from Neisseria meningitidis [11] and YgfY from Escherichia coli. [12] The SdhE protein is found on the mitochondrial membrane is it is important for creating energy via a process named the electron transport chain. [9]

Function Edit

The function of SdhE has been described as a flavinator of succinate dehydrogenase. SdhE works as a co-factor chaperone that incorporates FAD into SdhA. This results in SdhA flavinylation which is required for the proper function succinate dehydrogenase. Studies indicate that SdhE is required by bacteria in order to grow on succinate, using succinate as its only source of carbon and additionally for the function, of succinate dehydrogenase, a vital component of the electron transport chain which produces energy. [9]

Structure Edit

The structure of these proteins consists of a complex bundle of five alpha-helices, which is composed of an up-down 3-helix bundle plus an orthogonal 2-helix bundle. [12]

Protein interactions Edit

SdhE interacts with the catalytic subunit of the succinate dehydrogenase (SDH) complex. [13]

Human disease Edit

The human gene named SDH5, encodes for the SdhE protein. The gene itself is located in the chromosomal position 11q13.1. Loss-of-function mutations result in paraganglioma, a neuroendocrine tumour. [13]

History Edit

The recent studies which suggest SdhE is required for bacterial flavinylation contradict previous thoughts on SdhE. It was originally proposed that FAD incorporation into bacterial flavoproteins was an autocatalytic process. Recent studies now argue that SdhE is the first protein to be identified as required for flavinylation in bacteria. Historically, the SdhE protein was once considered a hypothetical protein. [9] YgfY was also thought to be involved in transcriptional regulation. [12]

All subunits of human mitochondrial SDH are encoded in nuclear genome. After translation, SDHA subunit is translocated as apoprotein into the mitochondrial matrix. Subsequently, one of the first steps is covalent binding of the FAD cofactor (flavinylation). This process seems to be regulated by some of the tricarboxylic acid cycle intermediates. Specifically, succinate, isocitrate and citrate stimulate flavinylation of the SDHA. [14] In case of eukaryotic Sdh1 (SDHA in mammals), another protein is required for process of FAD incorporation – namely Sdh5 in yeast, succinate dehydrogenase assembly factor 2 (SDHAF2) in mammal cells.

Before forming a heterodimer with subunit SDHB, some portion of SDHA with covalently bound FAD appears to interact with other assembly factor – SDHAF4 (Sdh8 in yeast). Unbound flavinylated SDHA dimerizes with SDHAF4 which serves as a chaperone. Studies suggest that formation of SDHA-SDHB dimer is impaired in absence of SDHAF4 so the chaperon-like assembly factor might facilitate interaction of the subunits. Moreover, SDHAF4 seems to prevent ROS generation via accepting electrons from succinate which can be still oxidized by unbound monomeric SDHA subunit. [7]

Fe-S prosthetic groups of the subunit SDHB are being preformed in the mitochondrial matrix by protein complex ISU. The complex is also thought to be capable of inserting the iron-sulphur clusters in SDHB during its maturation. The studies suggest that Fe-S cluster insertion precedes SDHA-SDHB dimer forming. Such incorporation requires reduction of cysteine residues within active site of SDHB. Both reduced cysteine residues and already incorporated Fe-S clusters are highly susceptible to ROS damage. Two more SDH assembly factors, SDHAF1 (Sdh6) and SDHAF3 (Sdh7 in yeast), seem to be involved in SDHB maturation in way of protecting the subunit or dimer SDHA-SDHB from Fe-S cluster damage caused by ROS. [7]

Assembly of the hydrophobic anchor consisting of subunits SDHC and SDHD remains unclear. Especially in case of heme b insertion and even its function. Heme b prosthetic group does not appear to be part of electron transporting pathway within the complex II. [15] The cofactor rather maintains the anchor stability.


Electron Transport Chain

In their reduced forms, NADH and FADH2 carry electrons to the electron transport chain in the inner mitochondrial membrane. They deposit their electrons at or near the beginning of the transport chain, and the electrons are then passed along from one protein or organic molecule to the next in a predictable series of steps. Importantly, the movement of electrons through the transport chain is energetically “downhill,” such that energy is released at each step. In redox terms, this means that each member of the electron transport chain is more electronegative (electron-hungry) that the one before it, and less electronegative than the one after [2] . NAD + , which deposits its electrons at the beginning of the chain as NADH, is the least electronegative, while oxygen, which receives the electrons at the end of the chain (along with H + ) to form water, is the most electronegative. As electrons trickle “downhill” through the transport chain, they release energy, and some of this energy is captured in the form of an electrochemical gradient and used to make ATP.


Watch the video: Cellular Respiration 3- Electron carriers (February 2023).