Calculated pH-Dependent Population and Protonation of Carbon-Monoxy-Myoglobin Conformers

The conversion of light energy into ion gradients across biological membranes is one of the most fundamental reactions in primary biological energy transduction. Recently, the structure of the first light-activated Na + pump, Krokinobacter eikastus rhodopsin 2 (KR2), was resolved at atomic resolution [Kato HE, et al. (2015) Nature 521: [48][49][50][51][52][53]. To elucidate its molecular mechanism for Na + pumping, we perform here extensive classical and quantum molecular dynamics (MD) simulations of transient photocycle states. Our simulations show how the dynamics of key residues regulate water and ion access between the bulk and the buried light-triggered retinal site. We identify putative Na + binding sites and show how protonation and conformational changes gate the ion through these sites toward the extracellular side. We further show by correlated ab initio quantum chemical calculations that the obtained putative photocycle intermediates are in close agreement with experimental transient optical spectroscopic data. The combined results of the ion translocation and gating mechanisms in KR2 may provide a basis for the rational design of novel light-driven ion pumps with optogenetic applications.bacterial ion pumps | bioenergetics | QM/MM | optogenetics | retinal P rimary biological energy conversion is based on the efficient capture and conversion of light and chemical energy into ion gradients across biological membranes (1, 2). The established gradients are used to thermodynamically drive energy-requiring processes, such as active transport and synthesis of adenosine triphosphate (ATP) (3, 4). The rhodopsin family of proteins catalyzes such reactions by harnessing the energy from retinal photoisomerization and deprotonation reactions, followed by conformational changes that further trigger the pumping of ions across the membrane (5). All previously known ion-pumping rhodopsins function either as inward chloride or outward proton pumps, but the structure of the first Na + pumping rhodopsin, Krokinobacter eikastus rhodopsin 2 (KR2) (6), was recently resolved (7,8). In the absence of Na + ions, KR2 functions as an outward proton pump, similarly to bacteriorhodopsin (bR), but under physiological conditions, KR2 pumps Na + out of the cell (6, 9).KR2 shares the heptahelical transmembrane (7TM) structure common to all microbial rhodopsins (Fig. 1A) (5,7,8). In contrast to bR, however, where a highly conserved Asp-Thr-Asp (DTD) motif is used to pump protons, KR2 employs a unique NDQ motif comprising residues Asn112, Asp116, and Gln123 (6). In bR, Asp85 and Asp96 function as proton acceptors and donors for the protonated Schiff base (PSB), respectively, whereas in KR2, Asn112 and Gln123 occupy these positions, and Asp116 replaces Thr89. In analogy to bR, it has been suggested that Gln123 aids in capturing ions from the solvent and that Asn112 might be part of a Na + binding site (6,10).Similarly to other microbial rhodopsins, four photocycle intermediates have been spectroscopically identified in KR2 (Fig. 1B) (6)...

Section: Methodsmentioning

confidence: 99%

Energetics and dynamics of a light-driven sodium-pumping rhodopsin

Suomivuori

Gámiz‐Hernández

Sundholm

et al. 2017

“…Therefore, it can be determined by the same methods as used for the calculation of pigment redox potentials in PPCs (see refs. 20 and 34), which are based on the solution of the linearized Poisson-Boltzmann equation (35,36) and a Monte Carlo procedure for the determination of protonation probabilities of titratable residues in the protein (18,19). For the nonequilibrium correction term, ⌬X corr (m) , one has to consider the interaction of the charge density difference between the S 1 and S 0 states of the pigment with the surrounding dielectric (21).…”

Section: Computational Proceduresmentioning

confidence: 99%

“…Our simulations take into account all these aspects, allowing us to unravel in detail the various contributions to site energy differences on the basis of a crystal structure. In addition, we consider conformational differences between pigments and the consequences of nonstandard protonation patterns resulting from protein-and environment-induced changes of acid-base equilibria of titratable residues (18)(19)(20). In the classical electrostatic part of the simulations, we calculate the free energy change of the PPC that occurs when the charge density of a pigment in its S 0 state is changed into that of the S 1 state, taking into account the nonequilibrium polarization (21) Author contributions: T.R.…”

mentioning

confidence: 99%

α-Helices direct excitation energy flow in the Fenna–Matthews–Olson protein

Müh

Madjet

Adolphs

et al. 2007

Self Cite

186

115

In photosynthesis, light is captured by antenna proteins. These proteins transfer the excitation energy with almost 100% quantum efficiency to the reaction centers, where charge separation takes place. The time scale and pathways of this transfer are controlled by the protein scaffold, which holds the pigments at optimal geometry and tunes their excitation energies (site energies). The detailed understanding of the tuning of site energies by the protein has been an unsolved problem since the first high-resolution crystal structure of a light-harvesting antenna appeared >30 years ago [Fenna RE, Matthews BW (1975) Nature 258:573-577].Here, we present a combined quantum chemical/electrostatic approach to compute site energies that considers the whole protein in atomic detail and provides the missing link between crystallography and spectroscopy. The calculation of site energies of the Fenna-Matthews-Olson protein results in optical spectra that are in quantitative agreement with experiment and reveals an unexpectedly strong influence of the backbone of two ␣-helices. The electric field from the latter defines the direction of excitation energy flow in the Fenna-Matthews-Olson protein, whereas the effects of amino acid side chains, hitherto thought to be crucial, largely compensate each other. This result challenges the current view of how energy flow is regulated in pigment-protein complexes and demonstrates that attention has to be paid to the backbone architecture.energy transfer ͉ light-harvesting ͉ optical spectra ͉ photosynthesis ͉ structure-based simulation P hotosynthesis is the fundamental biological process in which solar energy is converted into biomass. The first step is the capture of light by arrays of protein-bound dye molecules (pigments). These pigment-protein complexes (PPCs) are therefore termed light-harvesting complexes or antenna proteins (1). They transfer the excitation energy with high quantum yield to specialized PPCs, the reaction centers, where the energy is used to trigger the chemical modification of substrates. To guide the excitation energy flow in a certain direction there has to be an energy sink, that is, the pigments in the target region are required to absorb at lower energies than the initially excited chromophores. A complication of this simple picture arises from long-range electrostatic interactions between the local excitations (excitonic couplings), which are a prerequisite for energy transfer. These couplings cause the excited states of the PPC (exciton states) to be delocalized, that is, their electronic wave functions contain contributions of several pigments in the complex. Directed energy transport results from energetic relaxation transferring population between exciton states of different spatial extents. The latter depend crucially on excitonic couplings and site energies, so that the elucidation of energy-transfer mechanisms on the basis of spectroscopic data (2-4) and crystal structures (5-7) requires knowledge of both these quantities (8, 9), which are not direct...

“…The computation of the energetics of the protonation pattern of titratable residues and cofactors in proteins is based on the electrostatic continuum model, in which the linearized Poisson-Boltzmann (LPB) equation is solved by the program MEAD from Bashford and Karplus (36). To sample the ensemble of protonation patterns by a Monte Carlo (MC) method, we used our own program, KARLSBERG (37,38). The dielectric constant was set to P ϭ 4 inside the protein and W ϭ 80 for solvent and possible protein cavities.…”

Section: Computational Proceduresmentioning

confidence: 99%

How photosynthetic reaction centers control oxidation power in chlorophyll pairs P680, P700, and P870

Ishikita

Saenger²,

Biesiadka³

et al. 2006

Self Cite

107

110

At the heart of photosynthetic reaction centers (RCs) are pairs of chlorophyll a (Chla), P700 in photosystem I (PSI) and P680 in photosystem II (PSII) of cyanobacteria, algae, or plants, and a pair of bacteriochlorophyll a (BChla), P870 in purple bacterial RCs (PbRCs). These pairs differ greatly in their redox potentials for one-electron oxidation, E m. For P680, Em is 1,100 -1,200 mV, but for P700 and P870, E m is only 500 mV. Calculations with the linearized Poisson-Boltzmann equation reproduce these measured E m differences successfully. Analyzing the origin for these differences, we found as major factors in PSII the unique Mn 4Ca cluster (relative to PSI and PbRC), the position of P680 close to the luminal edge of transmembrane ␣-helix d (relative to PSI), local variations in the cd loop (relative to PbRC), and the intrinsically higher E m of Chla compared with BChla (relative to PbRC).electron transfer ͉ photosystem ͉ redox potential ͉ special pair ͉ electrostatic energy T he essence of photosynthetic reaction centers (RCs) of photosystem I (PSI) and photosystem II (PSII) of cyanobacteria, green algae, and plants, as well as of purple bacterial RCs (PbRCs), are two homologous protein subunits (D1, D2) in PSII, (L, M) in PbRC, and the C-terminal RC domains of subunits (A, B) in PSI. The polypeptide chains of these subunits and the C-terminal domains of PSI are folded into five transmembrane ␣-helices (TMHs) in a semicircular arrangement, and the two subunits in each RC are interlocked in a handshake motif with comparable topography and related by a pseudo-twofold symmetry axis (Fig. 1).We consider here the pair of chlorophyll a (Chla) in PSI (Chla P A/B in P700) and in PSII (Chla P D1/D2 in P680) and the pair of bacteriochlorophyll a (BChla) in PbRC (BChla P L/M in P870), where light-driven charge separation results in positively charged radicals P700 ϩ⅐ , P680 ϩ⅐ , and P870 ϩ⅐ , respectively. In PSI and PbRC, P700 ϩ⅐ and P870 ϩ⅐ are rereduced by small water-soluble proteins. By contrast, P680 ϩ⅐ in PSII is rereduced by a redoxactive tyrosine (D1-Tyr-161, Y Z ), which is subsequently reduced by electron transfer from the unique Mn 4 Ca cluster, where water is oxidized under release of atmospheric oxygen, protons, and electrons. Kinetic studies (1) and computations (2) yielded redox potentials for one-electron oxidation E m (P680) of 1,100-1,300 mV, high enough for P680 ϩ⅐ to act as an electron acceptor for the different Mn 4 Ca redox states. According to recent studies, P680 probably consists of the Chla pair P D1/D2 or the two adjacent accessory Chla, Chl D1/D2 (3).In contrast to PSII, with an unusually high E m (P680) of 1,100-1,300 mV (1, 2), the corresponding E m values in PbRC, E m (P870) ϭ 500 mV (4), and in PSI, E m (P700) ϭ 500 mV (5), are low. Part of these E m differences were associated with electronic coupling, which is weak between Chla in P D1/D2 but strong between Bchla in P L/M because of mutual overlap of BChla rings I. Indeed, in the PbRC mutant His(M202)Leu, where His-202 that coordinates...