Theoretical Study of the Energetics of Proton Pumping and Oxygen Reduction in Cytochrome Oxidase

The heme-copper oxygen reductases are redox-driven proton pumps. In the current work, the effects of mutations in a proposed exit pathway for pumped protons are examined in the ba 3 -type oxygen reductase from Thermus thermophilus , leading from the propionates of heme a 3 to the interface between subunits I and II. Recent studies have proposed important roles for His376 and Asp372, both of which are hydrogen-bonded to propionate-A of heme a 3 , and for Glu126 II (subunit II), which is hydrogen-bonded to His376. Based on the current results, His376, Glu126 II , and Asp372 are not essential for either oxidase activity or proton pumping. In addition, Tyr133, which is hydrogen-bonded to propionate-D of heme a 3 , was also shown not to be essential for function. However, two mutations of the residues hydrogen-bonded to propionate-A, Asp372Ile and His376Asn, retain high electron transfer activity and normal spectral features but, in different preparations, either do not pump protons or exhibit substantially diminished proton pumping. It is concluded that either propionate-A of heme a 3 or possibly the cluster of groups centered about the conserved water molecule that hydrogen-bonds to both propionates-A and -D of heme a 3 is a good candidate to be the proton loading site.

mentioning

confidence: 81%

Exploring the proton pump and exit pathway for pumped protons in cytochrome ba₃fromThermus thermophilus

Chang¹,

Choi

Vakkasoglu

et al. 2012

“…Biological applications have focused principally on the modeling of enzymatic catalysis and active-site chemistry (79)(80)(81)(82)(83)(84)(85)(86)(87)(88), although interesting investigations of other phenomena, such as cooperativity in backbone hydrogen bonding (89) and modeling of ␤-sheet formation propensities by a periodic DFT calculation (90), have been performed recently. The use of QM͞MM methods permits incorporation of the full protein environment, which is crucial in an important subset of cases, as has recently been shown in cytochrome P450 (79), for example.…”

Section: Applicationsmentioning

confidence: 99%

Ab initioquantum chemistry: Methodology and applications

Friesner

2005

304

230

This Perspective provides an overview of state-of-the-art ab initio quantum chemical methodology and applications. The methods that are discussed include coupled cluster theory, localized second-order Moller-Plesset perturbation theory, multireference perturbation approaches, and density functional theory. The accuracy of each approach for key chemical properties is summarized, and the computational performance is analyzed, emphasizing significant advances in algorithms and implementation over the past decade. Incorporation of a condensed-phase environment by means of mixed quantum mechanical͞molecular mechanics or self-consistent reaction field techniques, is presented. A wide range of illustrative applications, focusing on materials science and biology, are discussed briefly.coupled cluster ͉ density functional theory ͉ second-order Modler-Plesser perturbation theory ͉ mixed quantum͞molecular mechanics O ver the past three decades, ab initio quantum chemistry has become an essential tool in the study of atoms and molecules and, increasingly, in modeling complex systems such as those arising in biology and materials science. The underlying core technology is computational solution of the electronic Schrodinger equation; given the positions of a collection of atomic nuclei, and the total number of electrons in the system, calculate the electronic energy, electron density, and other properties by means of a well defined, automated approximation (a ''model chemistry''). The ability to obtain ''goodenough'' solutions to the electronic Schrodinger equation for systems containing tens, or even hundreds, of atoms has revolutionized the ability of theoretical chemistry to address important problems in a wide range of disciplines; the Nobel Prize awarded to John Pople and Walter Kohn in 1998 is a reflection of this observation.In its exact form, the electronic Schrodinger equation is a many-body problem, whose computational complexity grows exponentially with the number of electrons, and hence, a brute force solution is intractable. Hartree-Fock theory, a mean field approach, produces reasonable results for many properties but is incapable of providing a robust description of reactive chemical events in which electron correlation has a major role. Thus, a key problem has been the development of treatments of electron correlation that exhibit a tractable scaling in computational effort with the size of the system. The considerable progress that has been made along these lines is outlined below.Given a well defined theoretical framework of approximation, the next requirement is efficient computational implementation. Considerable sophistication is required to achieve acceptable accuracy and efficiency; the leading quantum chemistry programs are millions of lines of computer code, and mathematical algorithms to reduce formal scaling of computational effort with system size have an increasingly crucial role in meeting the challenge of handling complex system relevant to practical applications. Below, the most important comp...

“…3, [13][14][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)(18)(19)(20)(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).…”

mentioning

confidence: 99%

Analyzing the electrogenicity of cytochrome c oxidase

Kim

Warshel

2016

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...