Binding constants for a physiologic electron-transfer protein complex between methylamine dehydrogenase and amicyanin. Effects of ionic strength and bound copper on binding

Relaxation of structural constraints during Amicyanin unfolding

We study the thermal unfolding of amicyanin by quantifying the resiliency of the native state to structural perturbations. Three signatures characterizing stages of unfolding are identified. The first signature, lateral extension of the polypeptide chain, is calculated directly from the reported crystallographic data. Two other signatures, the radial displacement of each residue from Cu(II) and the angular spread in the chain as the protein unfolds, are calculated using crystallographic data in concert with a geometrical model we introduced previously (J.J. Kozak, H. B. Gray, R. A. Garza-López, J. Inorg. Biochem. 155(2016) 44-55). Particular attention is paid to the resiliency of the two beta sheets in amicyanin. The resiliency of residues in the near neighborhood of the Cu center to destabilization provides information on the persistence of the entatic state. Similarly, examining the resiliency of residues intercalated between structured regions (beta sheets, the alpha helix) provides a basis for identifying a "hydrophobic core." A principal focus of our study is to compare results obtained using our geometrical model with the experimental results (C. La Rosa, D. Milardi, D. M. Grasso, M. P. Verbeet, G. W. Canters, L. Sportelli, R. Guzzi, Eur. Biophy. J.30(8),(2002) 559-570) on the denaturation of amicyanin, and we show that our results support a classical model proposed by these authors.

The sole tryptophan of amicyanin enhances its thermal stability but does not influence the electronic properties of the type 1 copper site

The cupredoxin amicyanin possesses a single tryptophan residue, Trp45. Its fluorescence is quenched when copper is bound even though it is separated by 10.1Å. Mutation of Trp45 to Ala, Phe, Leu and Lys resulted in undetectable protein expression. A W45Y amicyanin variant was isolated. The W45Y mutation did not alter the spectroscopic properties or intrinsic redox potential of amicyanin, but increased the pKa value for the pH-dependent redox potential by 0.5 units. This is due to a hydrogen-bond involving the His95 copper ligand which is present in reduced W45Y amicyanin but not in native amicyanin. The W45Y mutation significantly decreased the thermal stability of amicyanin, as determined by changes in the visible absorbance of oxidized amicyanin and in the circular dichroism spectra for oxidized, reduced and apo forms of amicyanin. Comparison of the crystal structures suggests that the decreased stability of W45Y amicyanin may be attributed to the loss of a strong interior hydrogen bond between Trp45 and Tyr90 in native amicyanin which links two of the β-sheets that comprise the overall structure of amicyanin. Thus, Trp45 is critical for stabilizing the structure of amicyanin but it does not influence the electronic properties of the copper which quenches its fluorescence.

Amicyanin metal-site structure and interaction with MADH: PAC and NMR spectroscopy of Ag-, Cd-, and Cu-amicyanin

To investigate the structural control mechanisms in the metal site of amicyanin when interacting with MADH, redox-inactive Ag(+)- and Cd(2+)-substituted amicyanins were studied with perturbed angular correlations of gamma-rays (PAC) spectroscopy. PAC experiments on (111m)Cd-substituted amicyanin revealed two different metal-site structures, which are very likely in dynamic exchange on a ~5 ns timescale. Only one structure binds to MADH. The dissociation constants, K(d), are 9+/-2 microM with MADH(red) and 38+/-11 microM with MADH(ox), indicating that the Cd-amicyanin binding affinity is regulated by the MADH redox state. PAC experiments on (111)Ag-substituted amicyanin also showed two different forms of Ag-amicyanin, probably reflecting relaxation from Ag to Cd geometry. No binding of Ag-amicyanin to MADH could be observed with PAC, suggesting that the K(d) is larger than 43 microM, based on the 95% confidence limit. NMR revealed large chemical shift differences between native copper amicyanin and both metal-substituted forms. Affected residues are found up to 15 A away from the metal ion. The Ag(+)- and Cd(2+)-substituted amicyanins demonstrate no change in coordination as a function of pH, contrary to Cu(+)-amicyanin which shows protonation of the copper ligand His96 with p K(a)=6.8. It is concluded that, contrary to other blue copper proteins, Ag(+)-amicyanin is not a close mimic of Cu(+)-amicyanin, and that structural changes in the metal site have large effects on the affinity for the redox partner.

Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations

Protein-protein docking algorithms provide a means to elucidate structural details for presently unknown complexes. Here, we present and evaluate a new method to predict protein-protein complexes from the coordinates of the unbound monomer components. The method employs a low-resolution, rigid-body, Monte Carlo search followed by simultaneous optimization of backbone displacement and side-chain conformations using Monte Carlo minimization. Up to 10(5) independent simulations are carried out, and the resulting "decoys" are ranked using an energy function dominated by van der Waals interactions, an implicit solvation model, and an orientation-dependent hydrogen bonding potential. Top-ranking decoys are clustered to select the final predictions. Small-perturbation studies reveal the formation of binding funnels in 42 of 54 cases using coordinates derived from the bound complexes and in 32 of 54 cases using independently determined coordinates of one or both monomers. Experimental binding affinities correlate with the calculated score function and explain the predictive success or failure of many targets. Global searches using one or both unbound components predict at least 25% of the native residue-residue contacts in 28 of the 32 cases where binding funnels exist. The results suggest that the method may soon be useful for generating models of biologically important complexes from the structures of the isolated components, but they also highlight the challenges that must be met to achieve consistent and accurate prediction of protein-protein interactions.

ZDOCK: an initial-stage protein-docking algorithm

The development of scoring functions is of great importance to protein docking. Here we present a new scoring function for the initial stage of unbound docking. It combines our recently developed pairwise shape complementarity with desolvation and electrostatics. We compare this scoring function with three other functions on a large benchmark of 49 nonredundant test cases and show its superior performance, especially for the antibody-antigen category of test cases. For 44 test cases (90% of the benchmark), we can retain at least one near-native structure within the top 2000 predictions at the 6 degrees rotational sampling density, with an average of 52 near-native structures per test case. The remaining five difficult test cases can be explained by a combination of poor binding affinity, large backbone conformational changes, and our algorithm's strong tendency for identifying large concave binding pockets. All four scoring functions have been integrated into our Fast Fourier Transform based docking algorithm ZDOCK, which is freely available to academic users at http://zlab.bu.edu/~ rong/dock.

Tyr(30) of amicyanin is not critical for electron transfer to cytochrome c-551i: implications for predicting electron transfer pathways

A Pathways analysis of the methylamine dehydrogenase-amicyanin-cytochrome c-551i protein electron transfer (ET) complex predicts two sets of ET pathways of comparable efficiency from the type I copper of amicyanin to the heme of cytochrome c-551i. In one pathway, the electron exits copper via the Cys(92) copper ligand, and in the other, it exits via the Met(98) copper ligand. If the Pathways algorithm is modified to include contributions from the anisotropy of metal-ligand coupling, independent of differences in copper-ligand bond length, then the pathways via Cys(92) are predicted to be at least 100-fold more strongly coupled than the pathways via any of the other copper ligands. All of the favored pathways via Cys(92) include a through-space jump from Cys(92) to the side chain of Tyr(30). To determine whether or not the pathways via Cys(92) are preferentially used for ET, Tyr(30) was changed to other amino acid residues by site-directed mutagenesis. Some mutant proteins were very unstable suggesting a role for Tyr(30) in stabilizing the protein structure. Y30F and Y30I mutant amicyanins could be isolated and analyzed. For the Y30I mutant, the modified Pathways analysis which favors ET via Cys(92) predicts a decrease in ET rate of at least two orders of magnitude, whereas the standard Pathways analysis predicts no change in ET rate since ET via Met(98) is not affected. Experimentally, the ET rates of the Y30I and Y30F mutants were indistinguishable from that of wild-type amicyanin. Likely explanations for these observations are discussed as are their implications for predicting pathways for ET reactions of metalloproteins.

Methods of screening combinatorial libraries using immobilized or restrained receptors

The screening of combinatorial libraries for compounds with high affinity toward drug receptors is currently a major center of attention. We describe methods recently developed for library screening that involve "constrained" receptors (either immobilized onto a surface or restrained to a compartment by some physical means). These include affinity selection chromatography, ultrafiltration assays, the scintillation proximity assay, a variety of interfacial optical techniques (surface plasmon resonance and its relatives, among others), the quartz crystal microbalance, the jet ring cell, and new interferometric assays using porous silicon to immobilize the receptor. We note some trends in assay development involving assays of membrane-bound complexes, and the coupling of two analytical methods to expand the assay resolution.

Ligand binding to macromolecules or micelles: use of centrifugal ultrafiltration to measure low-affinity binding

We describe a method for estimating ligand binding to a macromolecular sample under conditions where this binding is of low affinity and must be measured under equilibrium conditions, without removal of the unbound ligand. The method is based on centrifugal ultrafiltration through a membrane with a molecular mass cut-off intermediate between that of the ligand and that of the target, and the amount of bound ligand is calculated from the difference between the (total) ligand in the concentrated sample and the (free) ligand in the ultrafiltrate. Centrifugal ultrafiltration makes it possible to separate free ligand from bound ligand (without changing its concentration) and to simultaneously concentrate the target (such that the proportion of bound ligand becomes significant, even under low-affinity binding conditions). We applied this technique, using Centricon 10 (Amicon) devices, to several cases (soluble proteins, intact membranes, detergent-solubilized proteins, and pure detergent micelles) and assessed its value with respect to the common artifacts that occur in other protocols involving protein retention on nitrocellulose filters (nonspecific ligand adsorption and protein denaturation).

The interaction of methanol dehydrogenase and its cytochrome electron acceptor

A fluorescence method is described for direct measurement of the interaction between methanol dehydrogenase (MDH) and its electron acceptor cytochrome cL. This has permitted a distinction to be made between factors affecting electron transfer and those affecting the initial binding or docking process. It was confirmed that the initial interaction is electrostatic, but previous conclusions with respect to the mechanism of EDTA inhibition have been modified. It is proposed that the initial 'docking' of MDH and cytochrome cL is by way of ionic interactions between lysyl residues on its surface and carboxylate groups on the surface of cytochrome cL. This interaction is not inhibited by EDTA, which we suggest acts by binding to nearby lysyl residues, thus preventing movement of the 'docked' cytochrome to its optimal position for electron transfer, which probably involves interaction with the hydrophobic funnel in the surface of MDH.

Complex formation with methylamine dehydrogenase affects the pathway of electron transfer from amicyanin to cytochrome c-551i

Methylamine dehydrogenase (MADH), amicyanin, and cytochrome c-551i are soluble redox proteins that form a complex in solution (Chen, L., Durley, R., Mathews, F. S., and Davidson, V. L. (1994) Science 264, 86-90), which is required for the physiologic electron transfer from the tryptophan tryptophylquinone cofactor of MADH to heme via the copper center of amicyanin. The reduction of cytochrome by amicyanin within the complex in solution has been demonstrated using rapid scanning stopped-flow spectroscopy. Electron transfer from free, uncomplexed, amicyanin to cytochrome c-551i occurs much more rapidly but only to a very small extent because the reaction is thermodynamically much less favorable when amicyanin is not associated with MADH (Gray, K. A., Davidson, V. L., and Knaff, D. B. (1988) J. Biol. Chem. 263, 13987-13990). These kinetic data suggest that amicyanin binding to cytochrome c-551i occurs at different sites when amicyanin is free and when it is in complex with MADH. A model for the interactions of these proteins is presented.

Electron transfer reactions between aromatic amine dehydrogenase and azurin

Binding and electron transfer reactions between the tryptophan tryptophylquinone (TTQ) enzyme, aromatic amine dehydrogenase (AADH), and the type I copper protein azurin have been characterized. In steady-state kinetic assays using azurin as an electron acceptor, it was observed that the apparent Km for azurin decreased with increasing ionic strength. These results are the opposite of what was observed for the reaction between the TTQ enzyme methylamine dehydrogenase (MADH) and amicyanin, despite the fact that in both cases the pairs of redox proteins are each acidic proteins. It was further demonstrated that azurin does not function as an effective electron acceptor for MADH, and that amicyanin does not function as an effective electron acceptor for AADH. Thus, while the two TTQ enzymes each use type I copper proteins as physiologic electron acceptors, there is a strong specificity for which copper protein serves as a redox partner. The kinetic parameters for the electron transfer reactions from reduced AADH to oxidized azurin were determined by stopped-flow spectroscopy. Different results were obtained depending upon whether AADH was reduced chemically with dithionite or with the substrate tyramine. The values for the limiting first-order apparent electron transfer rate constant (kET) at 30 degrees C were 4 and 102 s-1, respectively. Kinetically determined values of Kd also differed by a factor of 2.4. These data suggest that the incorporation of the substrate-derived amino group into the reduced TTQ of AADH significantly increases the apparent kET. The interaction between AADH and azurin was also quantitated using an ultrafiltration binding assay. This yielded a Kd of 300 microM for the AADH--azurin complex.(ABSTRACT TRUNCATED AT 250 WORDS)

Binding of monovalent cations to methylamine dehydrogenase in the semiquinone state and its effect on electron transfer

The binding of monovalent cations to methylamine dehydrogenase in the semiquinone state (MADHsq) at a site close to the tryptophan tryptophylquinone (TTQ) active center is demonstrated in experiments which show that the radical EPR signal of MADHsq is considerably broadened in the presence of Cs+, NH4+, and, to a smaller extent, Na+. The cations also stabilize the semiquinone state, as is evident from the increase of the EPR intensity they induce. On the basis of the optical absorbance spectra, two slightly different forms of MADHsq can be discerned. One form, with the main band at 425 nm, is observed at low pH and in the presence of NH4+, whereas the other, with the main band at 429 nm, is observed at high pH and in the presence of Cs+ or Na+. Stopped-flow studies of the oxidation by amicyanin of MADHred via MADHsq to MADHox show a strong stimulation of the first step by monovalent cations. It is shown that it is primarily the actual electron transfer rate, rather than the affinity of MADHred for amicyanin, that is affected by cations. Values for the dissociation constants of the monovalent cations for MADHred, estimated from the kinetic experiments, are higher than those that were previously determined for MADHox, and can be deduced to be higher than those for MADHsq as well. The results are discussed within the context of the electron transfer theory.

Kinetics of the reduction of wild-type and mutant cytochrome c-550 by methylamine dehydrogenase and amicyanin from Thiobacillus versutus

To elucidate the kinetic properties of the methylamine dehydrogenase (MADH) redox chain of Thiobacillus versutus the reduction of cytochrome c-550 by MADH and amicyanin has been studied. Under steady state conditions, the rate constants of the reactions have been determined as a function of the ionic strength, both for wild type cytochrome c-550 and for mutants in which the conserved residue Lys14 has been replaced as follows: Lys14-->Gln (mutant [K14Q]cytochrome c-550) and Lys14-->Glu (mutant [K14E]cytochrome c-550). The second-order rate constant of the reduction of cytochrome c-550 by MADH shows a biphasic ionic-strength dependence. At low ionic strength the rate constant remains unchanged (wild type) or increases ([K14Q]cytochrome c-550) with increasing ionic strength, while at high salt concentrations the rate constant decreases monotonically as the ionic strength increases. It is suggested that conformational freedom exists in the association complex and that this is favourable for electron transfer. [K14Q]cytochrome c-550 and [K14E]cytochrome c-550 are reduced at rates 20-fold and 500-fold slower than wild-type cytochrome c-550 by MADH, due to a lower association constant. It is concluded that MADH possesses a negative patch with which cytochrome c-550 associates. Lys14 plays an important role in the formation of the reaction complex. The midpoint potentials of wild-type and mutant cytochrome c-550 have been determined by using cyclic voltammetry. [K14Q]cytochrome c-550 and [K14E]cytochrome c-550 show an increase in E0 of only 2 mV and 8 mV, respectively, compared to wild-type cytochrome c-550 (241 mV at pH 8.1). [K14Q]cytochrome c-550 and [K14E]cytochrome c-550 cytochrome c-550 are reduced by amicyanin at rates that are only slightly faster than for wild-type cytochrome c-550. The difference is partly attributable to the change in E0. High ionic strength results in a threefold increase in the rate in all three cases. These results indicate that charge interactions do not play a major role in the formation of the amicyanin/cytochrome c-550 reaction complex, suggesting an interaction at the hydrophobic patch of amicyanin. The reduction of cytochrome c-550 by MADH can be inhibited by Zn(2+)-substituted amicyanin. Ag(+)-amicyanin, however, has little effect on the reduction rate. These results suggest that MADH has a much higher affinity for Cu(2+)-amicyanin (substrate) than for Cu(+)-amicyanin (product). On the basis of these findings the roles of the components of the MADH redox chain are discussed.

Kinetic and thermodynamic analysis of a physiologic intermolecular electron-transfer reaction between methylamine dehydrogenase and amicyanin

The quinoprotein methylamine dehydrogenase (MADH) and a type I copper protein, amicyanin, form a physiologic complex in which electrons are transferred from tryptophan tryptophylquinone to copper. The reoxidation of MADH by amicyanin has been studied by stopped-flow spectroscopy. The rate constant for the electron-transfer (ET) reaction and the dissociation constant for the complex have been determined at different temperatures. Marcus theory was used to calculate the distance, reorganizational energy, and electronic coupling for the intermolecular ET reaction. The ET reaction exhibited a large apparent reorganizational energy of approximately 225 kJ mol-1 (2.3 eV) and a coupling of approximately 11.7 cm-1. From X-ray crystallographic studies of an actual complex of these proteins from Paracoccus denitrificans [Chen, L., et al. (1992) Biochemistry 31, 4959-4964], it was possible to infer putative pathways of ET. The ET distance predicted by Marcus theory from kinetic data correlated reasonably well with the structural information. Thus, it has been possible to correlate ET theories with data from solution studies and a known structure for a naturally occurring ET reaction between soluble proteins.