Microscopic basis for kinetic gating in cytochrome c oxidase: insights from QM/MM analysis

Goyal, Puja; Yang, Shuo; Cui, Qiang

doi:10.1039/c4sc01674b

Cited by 44 publications

(44 citation statements)

References 108 publications

(290 reference statements)

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“…Protons are unlikely to be exchanged between the two water molecules within the physiologically relevant time scale. In addition, proton exchange through a long array of water molecules is seriously suppressed by the hydrogen bonds between the water molecules and the protein moiety (11). The present x-ray structure indicates that all of the water molecules in this array are hydrogen-bonded to the protein moiety.…”

Section: Resultsmentioning

confidence: 74%

The Mg2+-containing Water Cluster of Mammalian Cytochrome c Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle

Yano¹,

Muramoto

Shimada³

et al. 2016

Journal of Biological Chemistry

132

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Bovine heart cytochrome c oxidase (CcO) pumps four proton equivalents per catalytic cycle through the H-pathway, a protonconducting pathway, which includes a hydrogen bond network and a water channel operating in tandem. Protons are transferred by H 3 O ؉ through the water channel from the N-side into the hydrogen bond network, where they are pumped to the P-side by electrostatic repulsion between protons and net positive charges created at heme a as a result of electron donation to O 2 bound to heme a 3 . To block backward proton movement, the water channel remains closed after O 2 binding until the sequential four-proton pumping process is complete. Thus, the hydrogen bond network must collect four proton equivalents before O 2 binding. However, a region with the capacity to accept four proton equivalents was not discernable in the x-ray structures of the hydrogen bond network. The present x-ray structures of oxidized/reduced bovine CcO are improved from 1.8/1.9 to 1.5/1.6 Å resolution, increasing the structural information by 1.7/1.6 times and revealing that a large water cluster, which includes a Mg 2؉ ion, is linked to the H-pathway. The cluster contains enough proton acceptor groups to retain four proton equivalents. The redox-coupled x-ray structural changes in Glu 198 , which bridges the Mg 2؉ and Cu A (the initial electron acceptor from cytochrome c) sites, suggest that the Cu A -Glu 198 -Mg 2؉ system drives redox-coupled transfer of protons pooled in the water cluster to the H-pathway. Thus, these x-ray structures indicate that the Mg 2؉ -containing water cluster is the crucial structural element providing the effective proton pumping in bovine CcO.Cytochrome c oxidase (CcO) 3 reduces molecular oxygen (O 2 ) in a reaction coupled with a proton pumping process. After binding of O 2 to the O 2 reduction site (which includes two redox-active metal sites, heme a 3 and Cu B ), four electron equivalents are sequentially donated from cytochrome c via two additional redox active metal sites, Cu A and heme a. Each of the four electron transfers is coupled to the pumping of a single proton equivalent (1, 2).High resolution x-ray structural studies together with mutational analyses for bovine CcO show a possible proton pumping pathway, known as the H-pathway, which includes a hydrogen bond network and a water channel functioning in tandem (1, 2). The water channel provides access of water molecules (or H 3 O ϩ ions) inside the mitochondrial inner membrane (the N-side) to one end of the hydrogen bond network that extends to the outside of the mitochondrial inner membrane (the P-side). The hydrogen bond network interacts tightly with heme a by forming two hydrogen bonds between the formyl group of heme a and Arg 38 in the hydrogen bond network and between the A-ring propionate of heme a and a fixed water molecule in the hydrogen bond network (1, 2). The net positive charge increase in heme a, which occurs upon electron donation from heme a to the O 2 reduction site to be delocalized to the formyl and propionate gro...

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Section: Resultsmentioning

confidence: 74%

The Mg2+-containing Water Cluster of Mammalian Cytochrome c Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle

Yano¹,

Muramoto

Shimada³

et al. 2016

Journal of Biological Chemistry

132

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“…However, this sequence of reactions is inconsistent with the earlier proposal that the first PT is from the protonated E286 (33; see also refs. [44][45][46] solution to E286 (21,26), but this sequence of events is less likely based on our earlier results (41).…”

Section: Resultsmentioning

confidence: 98%

“…Apparently, there has been some progress in using structures in functional analyses (e.g., refs. 16,[24][25][26]. However, we still do not have a consistent model that correctly reproduces the pumping events, while preventing the back reaction.…”

mentioning

confidence: 99%

Analyzing the electrogenicity of cytochrome c oxidase

Kim

Warshel

2016

Proc. Natl. Acad. Sci. U.S.A.

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Measurements of voltage changes in response to charge separation within membrane proteins can offer fundamental information on spectroscopically "invisible" steps. For example, results from studies of voltage changes associated with electron and proton transfer in cytochrome c oxidase could, in principle, be used to discriminate between different theoretical models describing the molecular mechanism of proton pumping. Earlier analyses of data from these measurements have been based on macroscopic considerations that may not allow for exploring the actual molecular mechanisms. Here, we have used a coarse-grained model describing the relation between observed voltage changes and specific charge-transfer reactions, which includes an explicit description of the membrane, the electrolytes, and the electrodes. The results from these calculations offer mechanistic insights at the molecular level. Our main conclusion is that previously assumed mechanistic evidence that was based on electrogenic measurements is not unique. However, the ability of our calculations to obtain reliable voltage changes means that we have a tool that can be used to describe a wide range of electrogenic charge transfers in channels and transporters, by combining voltage measurements with other experiments and simulations to analyze new mechanistic proposals.electrogenicity | membrane potential | proton transfer | electron transfer C ytochrome c oxidase (CcO) couples the four-electron reduction of O 2 to water, where the released free energy is used to pump protons from the negative (N) to the positive (P) side of the membrane (1-5), leading to an electrochemical proton gradient that drives, for example, ATP synthesis. The elucidation of the structure of CcO (6-12), combined with experimental and theoretical studies (e.g., refs. 3, 13-15), has advanced the understanding of this intriguing system. Progress has been made in defining the conditions that would allow CcO to pump protons against a pH gradient (4, 16), in estimating the electrostatic energy of possible intermediates (17-21), in evaluating the energetics of the key water chains (22,23), and of a number of specific proton-transfer (PT) reactions (16). Furthermore, examination of the energetics of the overall pumping process has been performed by using a semimacroscopic model (16).However, the relationship between protein structure, the PT energetics, and detailed PT trajectories has not been established. Furthermore, to our knowledge, a consistent protonpumping mechanism purely based on structural information and thermodynamic considerations has not been presented. For example, we still cannot identity the primary acceptor for pumped protons, although the D propionate of heme a 3 (Prda3 in Fig. 1) is one of the most likely candidates for being at least a "transient" acceptor. Apparently, there has been some progress in using structures in functional analyses (e.g., refs. 16, 24-26). However, we still do not have a consistent model that correctly reproduces the pumping events, while prev...

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“…From a broader perspective, these observations demonstrate that ionization-resistant hydroxyl groups, such as serine and threonine (or other residues with a locally high pK a 48,49 ) can be H-bonded within a proton wire and still actively participate via deep proton tunneling. Wellaligned proton wires that are composed solely of water molecules are known to be extremely efficient charge carriers that can transport an excess proton on a sub-ps timescale 25 ; however, these water structures can be unstable, especially when long distances need to be traversed 50 .…”

Section: Discussionmentioning

confidence: 99%

“…It has been proposed that the hydroxyl residue must be protonated to -OH 2 + in order to make transport to the adjoining neutral water possible 17 , but such a protonation step has very low probability. Generally, when a classical approach is used, large barriers associated with high pK a residues in the protein interior 48,49 will lead to such slow rates that these residues must be excluded. In contrast, the experimental results presented here demonstrate that such residues can play an active role in proton wires via deep tunneling and suggest a natural way for the protein to control the direction of proton flow.…”

Section: Discussionmentioning

confidence: 99%

Wide-dynamic-range kinetic investigations of deep proton tunnelling in proteins

et al. 2016

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Abstract:Directional proton transport along "wires" that feed biochemical reactions in proteins is poorly understood. Amino acid residues with high pK a are seldom considered as active transport elements in such wires because of their large classical barrier for proton dissociation. Here we use the light-triggered proton wire of the green fluorescent protein (GFP) to study its ground electronic state proton transport kinetics, revealing a large temperature-dependent kinetic isotope effect. We show that "deep" proton tunneling between hydrogen-bonded oxygen atoms having a typical donor-acceptor distance of 2.7-2.8 Ǻ fully accounts for the rates at all temperatures, including the unexpectedly large value (2.5 10 9 s -1 ) found at room temperature. The rate limiting step in GFP is assigned to tunneling of the ionization-resistant serine hydroxyl proton. This suggests how high pK a residues within a proton wire can act as a "tunnel-diode" to kinetically trap protons and control the direction of proton flow.

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Microscopic basis for kinetic gating in cytochrome c oxidase: insights from QM/MM analysis

Cited by 44 publications

References 108 publications

The Mg2+-containing Water Cluster of Mammalian Cytochrome c Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle

The Mg2+-containing Water Cluster of Mammalian Cytochrome c Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle

Analyzing the electrogenicity of cytochrome c oxidase

Wide-dynamic-range kinetic investigations of deep proton tunnelling in proteins

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