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Ernst-Walter Knapp

Publications and source records attributed to Ernst-Walter Knapp.

At least 19 recordsLinked to original sources
PubMed2006

Connectivity independent protein-structure alignment: a hierarchical approach.

BACKGROUND: Protein-structure alignment is a fundamental tool to study protein function, evolution and model building. In the last decade several methods for structure alignment were introduced, but most of them ignore that structurally similar proteins can share the same spatial arrangement of secondary structure elements (SSE) but differ in the underlying polypeptide chain connectivity (non-sequential SSE connectivity). RESULTS: We perform protein-structure alignment using a two-level hierarchical approach implemented in the program GANGSTA. On the first level, pair contacts and relative orientations between SSEs (i.e. alpha-helices and beta-strands) are maximized with a genetic algorithm (GA). On the second level residue pair contacts from the best SSE alignments are optimized. We have tested the method on visually optimized structure alignments of protein pairs (pairwise mode) and for database scans. For a given protein structure, our method is able to detect significant structural similarity of functionally important folds with non-sequential SSE connectivity. The performance for structure alignments with strictly sequential SSE connectivity is comparable to that of other structure alignment methods. CONCLUSION: As demonstrated for several applications, GANGSTA finds meaningful protein-structure alignments independent of the SSE connectivity. GANGSTA is able to detect structural similarity of protein folds that are assigned to different superfamilies but nevertheless possess similar structures and perform related functions, even if these proteins differ in SSE connectivity.

Algorithms↗
PubMed2006

Function of two beta-carotenes near the D1 and D2 proteins in photosystem II dimers.

The antenna proteins in photosystem II (PSII) not only promote energy transfer to the photosynthetic reaction center (RC) but provide also an efficient cation sink to re-reduce chlorophyll a if the electron transfer (ET) from the Mn-cluster is inhibited. Using the newest PSII dimer crystal structure (3.0 A resolution), in which 11 beta-carotene molecules (Car) and 14 lipids are visible in the PSII monomer, we calculated the redox potentials (Em) of one-electron oxidation for all Car (Em(Car)) by solving the Poisson-Boltzmann equation. In each PSII monomer, the D1 protein harbors a previously unlocated Car (CarD1) in van der Waals contact with the chlorin ring of ChlZ(D1). Each CarD1 in the PSII dimer complex is located in the interface between the D1 and CP47 subunits, together with another four Car of the other PSII monomer and several lipid molecules. The proximity of Car bridging between CarD1 and plastoquinone/Q(A) may imply a direct charge recombination of Car+Q(A)-. The calculated Em(CarD1) and Em(ChlZ(D1)) are, respectively, 83 and 126 mV higher than Em(CarD2) and Em(ChlZ(D2)), which could explain why CarD2+ and ChlZ(D2)+ are observed rather than the corresponding CarD1+ and ChlZ(D1)+.

Cyanobacteria↗
PubMed2006

Electrostatic role of the non-heme iron complex in bacterial photosynthetic reaction center.

To elucidate the role of the non-heme iron complex (Fe-complex) in the electron transfer (ET) events of bacterial photosynthetic reaction centers (bRC), we calculated redox potentials of primary/secondary quinones Q(A/B) (E(m)(Q(A/B))) in the Fe-depleted bRC. Removing the Fe-complex, the calculated E(m)(Q(A/B)) are downshifted by approximately 220 mV/ approximately 80 mV explaining both the 15-fold decrease in ET rate from bacteriopheophytin (H(A)(-)) to Q(A) and triplet state occurrence in Fe-depleted bRC. The larger downshift in E(m)(Q(A)) relative to E(m)(Q(B)) increases the driving-energy for ET from Q(A) to Q(B) by 140 meV, in agreement with approximately 100 meV increase derived from kinetic studies.

Bacterial Proteins↗
PubMed2006

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

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, E(m) 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(4)Ca cluster (relative to PSI and PbRC), the position of P680 close to the luminal edge of transmembrane alpha-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).

Bacteriochlorophylls↗
PubMed2006

Function of redox-active tyrosine in photosystem II.

Water oxidation at photosystem II Mn-cluster is mediated by the redox-active tyrosine Y(Z). We calculated the redox potential (E(m)) of Y(Z) and its symmetrical counterpart Y(D), by solving the linearized Poisson-Boltzmann equation. The calculated E(m)(Y( )/Y(-)) were +926 mV/+694 mV for Y(Z)/Y(D) with the Mn-cluster in S2 state. Together with the asymmetric position of the Mn-cluster relative to Y(Z/D), differences in H-bond network between Y(Z) (Y(Z)/D1-His(190)/D1-Asn(298)) and Y(D) (Y(D)/D2-His(189)/D2-Arg(294)/CP47-Glu(364)) are crucial for E(m)(Y(Z/D)). When D1-His(190) is protonated, corresponding to a thermally activated state, the calculated E(m)(Y(Z)) was +1216 mV, which is as high as the E(m) for P(D1/D2). We observed deprotonation at CP43-Arg(357) upon S-state transition, which may suggest its involvement in the proton exit pathway. E(m)(Y(D)) was affected by formation of P(D2)(+) (but not P(D1)(+)) and sensitive to the protonation state of D2-Arg(180). This points to an electrostatic link between Y(D) and P(D2).

Manganese↗
PubMed2006

Energetics of a possible proton exit pathway for water oxidation in photosystem II.

The crystal structure of photosystem II (PSII) at 3.0-A resolution suggests that titratable residues on the lumenal side of D1/D2 and PsbO form a polar channel, which might serve as a proton exit pathway associated with water oxidation on the Mn-cluster. With full account of protein environment, we calculated the pK(a) of these residues by solving the linearized Poisson-Boltzmann equation. Along the prospective proton channel, the calculated pK(a) of titratable residues (namely via D1-Asp61, D1-Glu65, D2-Glu312, D2-Lys317 D1-Asp59, D1-Arg64, PsbO-Arg152, and PsbO-Asp224) monotonically increase from the Mn-cluster to the lumenal bulk side. We suggest that these residues form the exit pathway guiding protons, which are released at the Mn-cluster as a product of water oxidation, in an exergonic process out of PSII. Upon the S2 to S3 transition, CP43-Arg357 showed a dramatic deprotonation of ca. one H(+), suggesting that this residue is coupled to the redox states of the Mn-cluster and the tyrosine Y(Z). The calculated pK(a) values of 4.2-4.4 for D2-Glu312 and those of approximately 8-10.9 for D1-Asp59 and D1-Arg64 are indicative of the experimentally determined pK(a) values for inhibition of S-state transitions. Upon removal of the atomic coordinates of PsbO, the pK(a) of these residues are dramatically affected, indicating a significant role of PsbO in tuning the pK(a) of those residues in the proton exit pathway.

Binding Sites↗
PubMed2005

Stability and fluctuations of amide hydrogen bonds in a bacterial cytochrome c: a molecular dynamics study.

Molecular dynamics (MD) simulations on a bacterial cytochrome c were performed to investigate the lifetime and fluctuations of backbone hydrogen bonds and to correlate these data with protection factors for hydrogen exchange measured by NMR spectroscopy (Bartalesi et al. in Biochemistry, 42:10923-10930, 2003). The MD simulations provide a consistent pattern in that long lifetimes of hydrogen bonds go along with small amplitude fluctuations. In agreement with experiments, differences in stability were found with a rather flexible N-terminal segment as compared with a more rigid C-terminal part. Protection factors of backbone hydrogen exchange correlate strongly with the number of contacts but also with hydrogen-bond occupancy, hydrogen-bond survival times, as well as the inverse of fluctuations of backbone atoms and hydrogen-bond lengths derived from MD simulation data. We observed a conformational transition in the C-terminal loop, and significant motion in the N-terminal loop, which can be interpreted as being the structural units involved in the onset of the protein unfolding process in agreement with experimental evidence on mitochondrial cytochrome c.

Amides↗
PubMed2005

One-electron reduction potential for oxygen- and sulfur-centered organic radicals in protic and aprotic solvents.

We estimated one-electron reduction potentials of redox-active organic molecules for a spectrum of eight different functional groups (phenoxyl, p-benzoquinone, phenylthiyl, p-benzodithiyl, carboxyl, benzoyloxyl, carbthiyl, and benzoylthiyl) in protic (water) and aprotic (acetonitrile, N,N-dimethylacetamide) solvents. Electron affinities (EA) were evaluated in a vacuum with high level quantum chemical methods using Gaussian3-MP2 (G3MP2) and Becke 3 Lee, Yang, and Parr functional B3LYP with aug-cc-pVTZ basis set. To evaluate one-electron redox potentials, gas-phase free energies were combined with solvation energies obtained in a two-step computational approach. First, atomic partial charges were determined in a vacuum by the quantum chemical method B3LYP/6-31G(d,p). Second, solvation energies were determined, solving the Poisson equation with these atomic partial charges. Redox potentials computed this way, compared to experimental data for the 21 considered organic compounds in different solvents, yielded overall root-mean-square deviations of 0.058 and 0.131 V using G3MP2 or B3LYP to compute electronic energies, respectively, while B3LYP/6-31G(d,p) was used to compute solvation energies.

Journal Article↗
PubMed2005

Oxidation of the non-heme iron complex in photosystem II.

In photosystem II (PSII), the redox properties of the non-heme iron complex (Fe complex) are sensitive to the redox state of quinones (Q(A/)(B)), which may relate to the electron/proton transfer. We calculated the redox potentials for one-electron oxidation of the Fe complex in PSII [E(m)(Fe)] based on the reference value E(m)(Fe) = +400 mV at pH 7 in the Q(A)(0)Q(B)(0) state, considering the protein environment in atomic detail and the associated changes in protonation pattern. Our model yields the pH dependence of E(m)(Fe) with -60 mV/pH as observed in experimental redox titration. We observed significant deprotonation at D1-Glu244 in the hydrophilic loop region upon Fe complex oxidation. The calculated pK(a) value for D1-Glu244 depends on the Fe complex redox state, yielding a pK(a) of 7.5 and 5.5 for Fe(2+) and Fe(3+), respectively. To account for the pH dependence of E(m)(Fe), a model involving not only D1-Glu244 but also the other titratable residues (five Glu in the D-de loops and six basic residues near the Fe complex) seems to be needed, implying the existence of a network of residues serving as an internal proton reservoir. Reduction of Q(A/B) yields +302 mV and +268 mV for E(m)(Fe) in the Q(A)(-)Q(B)(0) and Q(A)(0)Q(B)(-) states, respectively. Upon formation of the Q(A)(0)Q(B)(-) state, D1-His252 becomes protonated. Forming Fe(3+)Q(B)H(2) by a proton-coupled electron transfer process from the initial state Fe(2+)Q(B)(-) results in deprotonation of D1-His252. The two EPR signals observed at g = 1.82 and g = 1.9 in the Fe(2+)Q(A)(-) state of PSII may be attributed to D1-His252 with variable and fixed protonation, respectively.

Amino Acids↗
PubMed2005

Electrostatic influence of PsaC protein binding to the PsaA/PsaB heterodimer in photosystem I.

The absence of the PsaC subunit in the photosystem I (PSI) complex (native PSI complex) by mutagenesis or chemical manipulation yields a PSI core (P700-F(X) core) that also lacks subunits PsaD and PsaE and the two iron-sulfur clusters F(A) and F(B), which constitute an integral part of PsaC. In this P700-F(X) core, the redox potentials (E(m)) of the two quinones A(1A/B) and the iron-sulfur cluster F(X) as well as the corresponding protonation patterns are investigated by evaluating the electrostatic energies from the solution of the linearized Poisson-Boltzmann equation. The B-side specific Asp-B558 changes its protonation state significantly upon isolating the P700-F(X) core, being mainly protonated in the native PSI complex but ionized in the P700-F(X) core. In the P700-F(X) core, E(m)(A(1A/B)) remains practically unchanged, whereas E(m)(F(X)) is upshifted by 42 mV. With these calculated E(m) values, the electron transfer rate from A(1) to F(X) in the P700-F(X) core is estimated to be slightly faster on the A(1A) side than that of the wild type, which is consistent with kinetic measurements.

Aspartic Acid↗
PubMed2005

Induced conformational changes upon Cd2+ binding at photosynthetic reaction centers.

Cd(2+) binding at the bacterial photosynthetic reaction center (bRC) from Rhodobacter sphaeroides is known to inhibit proton transfer (PT) from bulk solvent to the secondary quinone Q(B). To elucidate this mechanism, we calculated the pK(a) for residues along the water channels connecting Q(B) with the stromal side based on the crystal structures of WT-bRC and Cd(2+)-bound bRC. Upon Cd(2+) binding, we observed the release of two protons from His-H126/128 at the Cd(2+) binding site and significant pK(a) shifts for residues along the PT pathways. Remarkably, Asp-L213 near Q(B), which is proposed to play a significant role in PT, resulted in a decrease in pK(a) upon Cd(2+) binding. The direct electrostatic influence of the Cd(2+)-positive charge on these pK(a) shifts was small. Instead, conformational changes of amino acid side chains induced electrostatically by Cd(2+) binding were the main mechanism for these pK(a) shifts. The long-range electrostatic influence over approximately 12 A between Cd(2+) and Asp-L213 is likely to originate from a set of Cd(2+)-induced successive reorientations of side chains (Asp-H124, His-H126, His-H128, Asp-H170, Glu-H173, Asp-M17, and Asp-L210), which propagate along the PT pathways as a "domino" effect.

Binding Sites↗
PubMed2005

Control of quinone redox potentials in photosystem II: Electron transfer and photoprotection.

In O(2)-evolving complex Photosystem II (PSII), an unimpeded transfer of electrons from the primary quinone (Q(A)) to the secondary quinone (Q(B)) is essential for the efficiency of photosynthesis. Recent PSII crystal structures revealed the protein environment of the Q(A/B) binding sites. We calculated the plastoquinone (Q(A/B)) redox potentials (E(m)) for one-electron reduction with a full account of the PSII protein environment. We found two different H-bond patterns involving Q(A) and D2-Thr217, resulting in an upshift of E(m)(Q(A)) by 100 mV if the H bond between Q(A) and Thr is present. The formation of this H bond to Q(A) may be the origin of a photoprotection mechanism, which is under debate. At the Q(B) side, the formation of a H bond between D2-Ser264 and Q(B) depends on the protonation state of D1-His252. Q(B) adopts the high-potential form if the H bond to Ser is present. Conservation of this residue and H-bond pattern for Q(B) sites among bacterial photosynthetic reaction centers (bRC) and PSII strongly indicates their essential requirement for electron transfer function.

Electron Transport↗
PubMed2005

Redox potential of cytochrome c550 in the cyanobacterium Thermosynechococcus elongates.

Cytochrome c550 (cyt c550) from photosystem II (PSII) exists in the PSII-bound form but can be released from PSII by treatment with divalent cations or Tris, yielding the isolated form. We calculated heme redox potentials (Em) based on the crystal structures of cyt c550 by solving the Poisson-Boltzmann equation. In the isolated form, the calculated Em are -240 mV at pH 6.0 and -352 mV at pH 9.0. This pH-dependence is predominantly due to deprotonation of the heme-propionic group near Asn-49. In the PSII-bound form, the calculated E(m) was up-shifted by 160 mV versus the isolated form due to a conformational change of protein backbone, yielding Em=-84 mV.

Cyanobacteria↗
PubMed2005

Role of ions on structure and stability of a synthetic gramicidin ion channel in solution. A molecular dynamics study.

We performed a molecular dynamics (MD) simulation to the investigate structure and stability of a synthetic gramicidin-like peptide in solution with and without ions. The starting structures of the MD simulations were taken from two recently solved NMR structures of this peptide in isotropic solution, which forms stable monomers or dimers in the presence or absence of ions, respectively. The monomeric structure is channel-like and is assumed to be stabilized by the presence of two Cs(+) ions bound in the channel, each one close to one channel entrance. In our MD simulations, we observed how the Cs(+) ions bind in the channel formed by the monomeric gramicidin-like peptide using implicit solvent and explicit ions with a concentration of 2 M. MD simulations were performed with and without explicit ions but with an implicit solvent model defined by the generalized Born approximation, which was used to mimic the dielectric properties of the solvent and to speed up the computations.

Gramicidin↗
PubMed2005

Computational studies on imidazole heme conformations.

Density functional theory computations of heme with ionized propionic acid groups, axially coordinated with two imidazoles, were performed for different mutual orientations of the imidazole planes. Environmental influences from water or protein were considered with a continuum dielectric medium by solving the Poisson equation. In vacuum, optimized geometries yielded imidazole-heme conformations where the NH groups of imidazoles are oriented toward the heme propionic groups in agreement with data from crystal structures of heme proteins. Conformational free-energy dependencies of the mutual orientation of axially ligated imidazoles calculated in protein (epsilon=10) and water (epsilon=80) environments confirmed the vacuum results, albeit the energy difference between the preferred and the 180 degrees opposite orientations of the imidazole ligand decreased from 3.84 kcal/mol in vacuum to 2.35 and 2.40 kcal/mol in protein and water, respectively. Two main factors determine the imidazole orientation: (1) the direct intramolecular electrostatic interactions of propionic groups with the polar NH groups of imidazole and (2) the electrostatic interaction of the total dipole moment of the imidazole-heme complex with the reaction field. In vacuum, only the first type of interaction is present, while in a dielectric medium the latter effect becomes competitive at high dielectric constant, resulting in a decrease of the orientational preference. Interestingly, the orientational preference of the imidazole axially ligated to heme becomes even more pronounced, if the negatively charged propionates are neutralized by counter charges that mimic salt bridges or protonation of the propionates.

Heme↗
PubMed2005

Redox potentials of chlorophylls in the photosystem II reaction center.

Water oxidation generating atmospheric oxygen occurs in photosystem II (PSII), a large protein-pigment complex located in the thylakoid membrane. The recent crystal structures at 3.2 and 3.5 A resolutions provide novel details on amino acid side chains, especially in the D1/D2 subunits. We calculated the redox potentials for one-electron oxidation of the chlorophyll a (Chla) molecules in PSII, considering the protein environment in atomic detail. The calculated redox potentials for the dimer Chla (P(D1/D2)) and accessory Chla (Chl(D1/D2)) were 1.11-1.30 V relative to the normal hydrogen electrode at pH 7, which is high enough for water oxidation. The D1/D2 proteins and their cofactors contribute approximately 390 mV to the enormous upshift of 470 mV compared to the redox potential of monomeric Chla in dimethylformamide. The other subunits are responsible for the remaining 80 mV. The high redox potentials of the two accessory Chla Chl(D1/D2) suggests that they also participate in the charge separation process.

Chlorophyll↗
PubMed2005

Redox potentials of chlorophylls and beta-carotene in the antenna complexes of photosystem II.

Electron transfer (ET) processes in reaction centers (RC) of photosystem II (PSII) are prerequisites of oxygen generation. They are promoted by energy transfer from antenna to RC. Here, we calculated the redox potentials of chlorophylla/beta-carotene (Chla/Car) in PSII CP43/CP47 antenna complexes, solving the linearized Poisson-Boltzmann (LPB) equation based on the PSII crystal structure. The majority of antenna Chla redox potentials for reduction/oxidation were lower than those of RC Chla. Hence, ET events with excess electrons remain localized in the RC. Simultaneously antenna Chla can serve as an efficient cation sink to rereduce RC Chla if normal PSII function is inhibited. Especially three antenna Chla (Chl-47, Chl-18, and Chl-12) and two Car bridging the space between Chl(Z(D1)) and cytochrome (cyt) b559 have the same level of oxidation redox potential. Together with Chl(Z(D2)) they form an electron hole transfer pathway and temporary storage device guiding from the oxidized P680(+.) Chla to the cyt b559. This path may play a photoprotective role as efficient electron hole quencher.

Chlorophyll↗