Role of arginine 67 in the stabilization of chymotrypsin inhibitor 2: examination of amide proton exchange rates and denaturation thermodynamics of an engineered protein

Structural stability as a probe for molecular evolution of homologous albumins studied by spectroscopy and bioinformatics

Equilibrium unfolding by guanidinium hydrochloride (GuHCl) and urea as well as evolutionary trends of two homologous albumins, pig serum albumin (PSA) and rabbit serum albumin (RSA), has been studied with circular dichroism, tryptophanyl fluorescence and bioinformatics. GuHCl cannot distinguish the contribution of electrostatic interactions to the proteins which were otherwise effectively monitored by urea. Higher differences in free energy changes due to urea than GuHCl show electrostatic interactions among charged amino acids are possibly responsible for higher structural stability of RSA in comparison to PSA. From the sequence of HSA and RSA, deletion of arginine at position 117 and the presence of one extra tryptophan at position 135 may possess some clue for lesser stability of PSA. Here, for comparison, chemical unfolding data of HSA and BSA had been taken into consideration. We found that thermodynamically RSA and PSA are closer to HSA and BSA, respectively, in accordance with their sequence homologies. Taxonomically, rabbit belongs to lagomorph which is closer to hominids than ungulates. Hence, on the basis of these thermodynamic data of protein denaturation of different species we can use this new approach to analyze the phylogenetic relationship among the major clades of eutherian mammals to obtain their evolutionary trends.

A holistic molecular docking approach for predicting protein-protein complex structure

A holistic protein-protein molecular docking approach, HoDock, was established, composed of such steps as binding site prediction, initial complex structure sampling, refined complex structure sampling, structure clustering, scoring and final structure selection. This article explains the detailed steps and applications for CAPRI Target 39. The CAPRI result showed that three predicted binding site residues, A191HIS, B512ARG and B531ARG, were correct, and there were five submitted structures with a high fraction of correct receptor-ligand interface residues, indicating that this docking approach may improve prediction accuracy for protein-protein complex structures.

Cores and pH-dependent dynamics of ferredoxin-NADP+ reductase revealed by hydrogen/deuterium exchange

NMR-detected hydrogen/deuterium (H/D) exchange of amide protons is a powerful way for investigating the residue-based conformational stability and dynamics of proteins in solution. Maize ferredoxin-NADP(+) reductase (FNR) is a relatively large protein with 314 amino acid residues, consisting of flavin adenine dinucleotide (FAD) and nicotinamide adenine dinucleotide phosphate (NADP(+))-binding domains. To address the structural stability and dynamics of FNR, H/D exchange of amide protons was performed using heteronuclear NMR at pD(r) values 8.0 and 6.0, physiologically relevant conditions mimicking inside of chloroplasts. At both pD(r) values, the exchange rate varied widely depending on the residues. The profiles of protected residues revealed that the highly protected regions matched well with the hydrophobic cores suggested from the crystal structure, and that the NADP(+)-binding domain can be divided into two subdomains. The global stability of FNR obtained by H/D exchange with NMR was higher than that by chemical denaturation, indicating that H/D exchange is especially useful for analyzing the residue-based conformational stability of large proteins, for which global unfolding is mostly irreversible. Interestingly, more dynamic conformation of the C-terminal subdomain of the NADP(+)-binding domain at pD(r) 8.0, the daytime pH in chloroplasts, than at pD(r) 6.0 is likely to be involved in the increased binding of NADP(+) for elevating the activity of FNR. In light of photosynthesis, the present study provides the first structure-based relationship of dynamics with function for the FNR-type family in solution.

Accelerated design of bioconversion processes using automated microscale processing techniques

Microscale processing techniques are rapidly emerging as a means to increase the speed of bioprocess design and reduce material requirements. Automation of these techniques can reduce labour intensity and enable a wider range of process variables to be examined. This article examines recent research on various individual microscale unit operations including microbial fermentation, bioconversion and product recovery techniques. It also explores the potential of automated whole process sequences operated in microwell formats. The power of the whole process approach is illustrated by reference to a particular bioconversion, namely the Baeyer-Villiger oxidation of bicyclo[3.2.0]hept-2-en-6-one for the production of optically pure lactones.

A single disulfide bond restores thermodynamic and proteolytic stability to an extensively mutated protein

The potential for engineering stable proteins with multiple amino acid substitutions was explored. Eleven lysine, five methionine, two tryptophan, one glycine, and three threonine substitutions were simultaneously made in barley chymotrypsin inhibitor-2 (CI-2) to substantially improve the essential amino acid content of the protein. These substitutions were chosen based on the three-dimensional structure of CI-2 and an alignment of homologous sequences. The initial engineered protein folded into a wild-type-like structure, but had a free energy of unfolding of only 2.2 kcal/mol, considerably less than the wild-type value of 7.5 kcal/mol. Restoration of the lysine mutation at position 67 to the wild-type arginine increased the free energy of unfolding to 3.1 kcal/mol. Subsequent cysteine substitutions at positions 22 and 82 resulted in disulfide bond formation and a protein with nearly wild-type thermodynamic stability (7.0 kcal/mol). None of the engineered proteins retained inhibitory activity against chymotrypsin or elastase, and all had substantially reduced inhibitory activity against subtilisin. The proteolytic stabilities of the proteins correlated with their thermodynamic stabilities. Reduction of the disulfide bond resulted in substantial loss of both thermodynamic and proteolytic stabilities, confirming that the disulfide bond, and not merely the cysteine substitutions, was responsible for the increased stability. We conclude that it is possible to replace over a third of the residues in CI-2 with minimal disruption of stability and structural integrity.

Conformation and stability of barley chymotrypsin inhibitor-2 (CI-2) mutants containing multiple lysine substitutions

A major goal of agricultural biotechnology is to increase the nutritional value of maize seed through the expression of heterologous proteins enriched in lysine. One promising candidate is barley chymotrypsin inhibitor-2 (CI-2), a plant protein that has been extensively characterized with respect to structure and function. Based on the tertiary structure of wild-type (WT) CI-2, five mutants with lysine contents ranging from 20 to 25 mol percent were designed, expressed in Escherichia coli and purified by ion exchange and gel permeation chromatography. Inasmuch as previous transgenic experiments suggested that proper folding and stability may be essential for in vivo accumulation of the engineered proteins in plant cells, we first undertook an in vitro study of the conformation and thermodynamic stability of the CI-2 mutants in order to select an ideal candidate for plant expression. Mutant and WT CI-2 proteins had similar circular dichroism spectra, suggesting similar secondary structures. However, differences in the accessibility of the sole tryptophan residue, Trp24, indicated that the local conformation differed among the mutants. The thermodynamic stability of the mutants ranged from <2 to 4.9 kcal/mol compared with approximately 7 kcal/mol for the wild-type protein. In conjunction with proteolytic stability studies, we have identified one mutant that has the potential to be expressed in a stable manner in plant cells.

Structural and kinetic analysis of drug resistant mutants of HIV-1 protease

Mutants of HIV-1 protease that are commonly selected on exposure to different drugs, V82S, G48V, N88D and L90M, showed reduced catalytic activity compared to the wild-type protease on cleavage site peptides, CA-p2, p6pol-PR and PR-RT, critical for viral maturation. Mutant V82S is the least active (2-20% of wild-type protease), mutants N88D, R8Q, and L90M exhibit activities ranging from 20 to 40% and G48V from 50 to 80% of the wild-type activity. In contrast, D30N is variable in its activity on different substrates (10-110% of wild-type), with the PR-RT site being the most affected. Mutants K45I and M46L, usually selected in combination with other mutations, showed activities that are similar to (60-110%) or greater than (110-530%) wild-type, respectively. No direct relationship was observed between catalytic activity, inhibition, and structural stability. The mutants D30N and V82S were similar to wild-type protease in their stability toward urea denaturation, while R8Q, G48V, and L90M showed 1.5 to 2.7-fold decreased stability, and N88D and K45I showed 1.6 to 1.7-fold increased stability. The crystal structures of R8Q, K45I and L90M mutants complexed with a CA-p2 analog inhibitor were determined at 2.0, 1.55 and 1.88 A resolution, respectively, and compared to the wild-type structure. The intersubunit hydrophobic contacts observed in the crystal structures are in good agreement with the relative structural stability of the mutant proteases. All these results suggest that viral resistance does not arise by a single mechanism.

Second-order kinetic analysis of IAsys biosensor data: its use and applicability

The kinetic analysis of IAsys biosensor association data usually relies upon the assumption of constant ligate concentration. In certain circumstances this assumption may no longer be valid. In a similar vein, the analysis of the dissociation phase assumes the concentration of ligate to be negligible in the liquid phase-an assumption that may not be sustainable for high-affinity interactions. In this paper we derive analytical solutions of the second-order differential kinetic equations for the association and dissociation phases, together with a binding isotherm that also allows for changes in concentration of both the ligand and the ligate. Using these equations it is possible to determine the conditions under which the pseudo-first-order assumption ceases to be valid. It is found that the effect of ligate depletion on the association rate constant becomes significant only when binding low ligate concentrations to ligand on surfaces with high binding capacities or high affinities. Similarly, the rebinding in the dissociation phase is dependent upon the affinity and the ligand capacity together with the starting dissociation response compared to the capacity. Finally, depletion also affects the form of the binding isotherm, particularly in situations involving high matrix capacities for ligate and high-affinity interactions.

Folding intermediates of wild-type and mutants of barnase. II. Correlation of changes in equilibrium amide exchange kinetics with the population of the folding intermediate

There is an unanswered question from previous studies of 1H/2H-exchange of amide protons of barnase. Under certain conditions, there is a relatively abrupt change from EX2 towards EX1 kinetics as the temperature is slightly increased. The change in kinetics for different mutants is not directly related to their changes in stability. We have measured the stability of the folding intermediate of barnase (I) in 2H2O under a variety of conditions and calculated its population at different temperatures. The change in kinetics correlates with the change in the population of the folding intermediate. At higher temperatures and pH, the free energy of I becomes higher than that of the denatured state, D, and the kinetics becomes EX1. The data fit a simple kinetic scheme. Such changes in kinetics may be used to detect the presence of intermediates in the folding reaction at equilibrium in native conditions, but cannot distinguish whether they are on or off-pathway.

Hydrogen exchange and protein folding

Amide hydrogen-deuterium exchange is a sensitive probe of the structure, stability and dynamics of proteins. The significant increase in the number of small, model proteins that have been studied has allowed a better understanding of the structural fluctuations that lead to hydrogen exchange. Recent technical advances enable the methodology to be applied to the study of protein-protein interactions in much larger, more complex systems.

Amide hydrogen exchange and internal dynamics in the chemotactic protein CheY from Escherichia coli

The backbone internal dynamics of the wild-type 129 amino acid alpha/beta parallel protein CheY and its double mutant F14N/P110G are analysed here by the hydrogen-exchange method. The F14N mutation is known to stabilise the protein and to accelerate refolding while P110G is destabilising and accelerates unfolding. We first assigned and characterised the double mutant by nuclear magnetic resonance (NMR), to try and discover any possible conformational change induced by the two mutations. The main difference between the two proteins is a favourable N-capping interaction of the newly introduced Asn14 side-chain at the beginning of the first alpha-helix (alpha-helix A). Second, we have measured the exchange rates in the wild-type and mutant CheY. In the first case the observed protection factors are slightly dispersed around an average value. According to their distribution in the structure, protein stability is highest on one face of the central beta-sheet, in the surroundings of the main hydrophobic core formed by side-chains of residues in beta-strands I, II and III and helices A and E. The mutations in the double mutant protein affect two distinct subdomains differently (from beta-strand I to III and from alpha-helix C to the end). In the second subdomain the number of protected protons is reduced with respect to those in the wild-type. This differential behaviour can be explained by a selective decrease in stability of the second folding subdomain produced by the P110G mutation and the opposite effect in the first subdomain, produced by the F14N mutation. alpha-Helix A, which is involved together with beta-strands I and III in the folding nucleus of CheY, shows the largest protection factors in both proteins.

Hydrogen exchange in chymotrypsin inhibitor 2 probed by mutagenesis

Two-dimensional NMR spectroscopy has been used to monitor hydrogen-deuterium exchange in chymotrypsin inhibitor 2. Application of two independent tests has shown that at pH 5.3 to 6.8 and 33 to 37 degrees C, exchange occurs via an EX2 limit. Comparison of the exchange rates of a number of mutants of CI2 with those of wild-type identifies the pathway of exchange, whether by local breathing, global unfolding or a mixture of the two pathways. For a large number of residues, the exchange rates were unaffected by mutations which destabilized the protein by up to 1.9 kcal mol(-1), indicating that exchange is occurring through local fluctuations of the native state. A small number of residues were found for which the mutations had the same effect on the rate constants for exchange as on the equilibrium constant for unfolding, indicating that these residues exchange by global unfolding. These are residues that have the slowest exchange rates in the wild-type protein. We see no correspondence between these residues and residues involved in the nucleation site for the folding reaction identified by protein engineering studies. Rather, the exchange behaviour of CI2 is determined by the native structure: the most protected amide protons are located in regions of hydrogen bonding, specifically the C terminus of the alpha-helix and the centre of the beta-sheet. A number of the most slowly exchanging residues are in the hydrophobic core of the protein.

Ligand loading at the surface of an optical biosensor and its effect upon the kinetics of protein-protein interactions

Optical biosensors are finding increasing use in the determination of kinetic and equilibrium constants for a variety of biomolecular interactions. Usually these biosensors require one biomolecule, the ligand, to be covalently attached to a hydrogel matrix which itself is bonded to the sensing surface. The ligands partner, the ligate, then binds from solution resulting in a measurable change in response which the instrument records as a function of time. Although in many cases, optical biosensors are used in order to obtain parameters that relate to interactions in solution, it is becoming clear that measurements involving the interaction of ligate with immobilized ligands on surfaces require careful experimental design. Here we report on how the density of ligand loading within the hydogel matrix affects the measured interaction kinetics. It is found that crowding of ligand within this matrix results in a significant reduction in the measured association rate constant, with a corresponding effect in the calculated overall affinity. However, measurements at low ligand loadings show association rate constants that are comparable to those measured in solution. Clearly, where this comparison is required, it is important to perform measurements under such conditions.

Energetic and entropic factors determining binding affinity in protein-ligand complexes

Understanding of non-covalent interactions in protein-ligand complexes is essential in modern biochemistry and should contribute toward the discovery of new drugs. The affinity of a ligand toward its receptor falls into a range of 10-80 kJ/mol. It is related to the binding constant and corresponds to a free energy. Accordingly enthalpic and entropic effects determine binding affinity. Hydrogen bonds and lipophilic contacts are the most important contributions to protein-ligand interactions. They are governed by changes in entropy and enthalpy. Solvation and desolvation effects either of the ligand and the protein binding site play a key role in the binding process. Prerequisite for a quantitative description and subsequently for a prediction of protein-ligand interactions is a partitioning in additive group contributions. In many cases, this additivity seems to be a good approximation, however, phenomena such as conformational pre-organizations give rise for a non-additive behavior. Flexibility and mobility of the bound ligand influence binding affinity. The rare experiments separating enthalpic and entropic contributions to the binding affinity sometimes reveal surprisings results, e.g. the loss of a hydrogen bond parallels with a loss in entropy.

Complete amino acid sequences of two trypsin inhibitors from buckwheat seed

The major trypsin isoinhibitors from seed extracts of buckwheat (Fagopyrum esculentum Mönch) were purified by affinity chromatography, anion exchange chromatography, anion exchange HPLC and reversed-phase HPLC, and the complete amino acid sequences of two isoinhibitors, BTI-1 and BTI-2, were established by automated Edman degradation. Each isoinhibitor consists of a single polypeptide chain of 69 amino acids, including two Cys residues. The N-terminal sequence of a third isoform, BTI-3, was also determined. The buckwheat trypsin isoinhibitors exhibit clear sequence similarities with the potato chymotrypsin inhibitor I family of serine proteinase inhibitors.

Conformational stability and catalytic activity of HIV-1 protease are both enhanced at high salt concentration

The activity of human immunodeficiency virus protease is markedly increased at elevated salt concentration. The structural basis of this effect has been explored by several independent methods by using both the wild-type enzyme and its triple mutant (Q7K/L33I/L63I) (Mildner, A. M., Rothrock, D. J., Leone, J. W., Bannow, C. A., Lull, J. M., Reardon, I. M., Sarcich, J. L., Howe, W. J., Tomich, C.-S. C., Smith, C. W., Heinrikson, R. L., and Tomasselli, A. G. (1994) Biochemistry 33, 9405-9413), designed to better resist autolysis. Monitoring the intrinsic fluorescence of the two enzymes during urea-mediated denaturation has shown that at high NaCl concentration, both the conformational stability ( DeltaG0) and the transition midpoint (D1/2) between the folded and unfolded states increase, indicating that the salt stabilizes the enzyme structure. These equilibrium data are supported by kinetic studies on the urea-mediated unfolding by measuring fluorescence change, red shifting in the maximum of the emission spectrum, and far- and near-UV CD. The salt effects observed in urea-mediated unfolding reactions prevail upon heat denaturation. All these findings support the existence of a two-state equilibrium between the folded and unfolded proteins. The pH dependence of fluorescence intensity indicated that the conformation of human immunodeficiency virus type 1 protease should change in the catalytically competent pH region. It is concluded that preferential hydration stabilizes the protease structure in the presence of salt, providing entropic contribution to enhance the catalytic activity.

Synthesis of a mixture of cyclic peptides based on the Bowman-Birk reactive site loop to screen for serine protease inhibitors

A peptide mixture containing 21 peptide sequences has been constructed to test the Bowman-Birk inhibitor reactive-site loop motif as the basis of inhibition for a range of serine proteases. The 21 peptides are all based on an 11 amino acid sequence designed from a Bowman-Birk like inhibitor reactive-site loop. Variation has been introduced at the P1 site of the loop, which has been randomised to include all the natural L-amino acids (except for cysteine), plus the non-natural L-amino acids ornithine and norleucine, The mixture of peptides was screened for specific binding to immobilised porcine pancreatic elastase, subtilisin BPN', alpha-chymotrypsin, trypsin, anhydro-alpha-chymotrypsin and anhydrotrypsin. Five peptides from the mixture bind to alpha-chymotrypsin, two of which also bind to anhydro-alpha-chymotrypsin, and two peptides bind trypsin, neither of which binds to anhydro-trypsin. The competitive inhibition constants (K(i)) and the rates of proteolytic hydrolysis of the individual peptides with their respective enzymes were determined. The rates of hydrolysis were found to vary widely and show little correlation with the K(i) values. In the case of the alpha-chymotrypsin inhibitors, the peptides with the lowest K(i) (0.1-0.05 mM) were the only peptides that bound to anhydro-alpha-chymotrypsin. However, no peptides bound to anhydrotrypsin, suggesting a fundamental difference in the way that alpha-chymotrypsin and trypsin are inhibited by these cyclic peptides.

Expression and kinetic characterization of barley chymotrypsin inhibitors 1a and 1b

The genes for chymotrypsin inhibitors 1a and 1b (CI-1a and CI-1b) from barley have been expressed in E. coli, and the CI-1a and CI-1b proteins purified. These proteins, although highly homologous, differ in the active site region at P2, P1' and P3' (Schechter and Berger nomenclature), and so might be expected to have differing specificities. Despite this, analysis of the inhibition kinetics showed that each displayed very similar kinetic behaviour when tested against a range of proteinases. The specificity of the CI-1 proteins is different to that of the other main barley inhibitor, CI-2, and Ki values are found to follow the series subtilisin Carlsberg < neutrophil elastase approximately subtilisin BPN' << chymotrypsin. Only very weak inhibition is found of trypsin, and pancreatic elastase is not measurably inhibited. For the proteinases inhibited most strongly, characteristic slow-binding inhibition kinetics were observed, whereas classical inhibition applied to the weaker interactions. The results are consistent with the major determinant of specificity being the P1 residue of the inhibitor, which is the same in both CI-1a and CI-1b. Consistent with this, is the similar spectrum of specificity found for the homologous inhibitor eglin c from leech, which has the same P1 residue. Both the CI-1 proteins are found to be less stable than CI-2, with CI-1a being significantly less stable than CI-1b as measured by guanidinium hydrochloride unfolding experiments. Possible reasons for the reduced stability are discussed in view of the sequence differences between CI-1a, CI-1b and CI-2.

Primary structure and specificity of the major serine proteinase inhibitor of amaranth (Amaranthus caudatus L.) seeds

A novel member of the potato inhibitor I family of serine proteinase inactivating proteins has been isolated from seeds of grain amaranth (Amaranthus caudatus L.) and characterized. The mature form of the amaranth trypsin/subtilisin inhibitor (ATSI) with pI approximately 8.3 and molecular mass 7887 Da contains 69 amino acids in a sequence showing 33-51% identity with members of the inhibitor I family from other plant families. A minor form with pI approximately 7.8 and same inhibitory properties lacked the N-terminal dipeptide Ala-Arg. In accordance with the reactive-site bond Lys45-Asp46, which was identified by specific cleavage on a subtilisin column, ATSI is a potent inhibitor of trypsin (Ki approximately 0.34 nM) and more weakly of plasmin (Ki approximately 38 nM) and Factor XIIa (Ki approximately 440 nM). However, ATSI also inactivates chymotrypsin (Ki approximately 0.41 nM), cathepsin G (Ki approximately 122 nM) and several alkaline microbial proteinases, including subtilisin NOVO (Ki approximately 0.37 nM). Interestingly, ATSI contains a Trp residue instead of the highly conserved Arg in position 53 (P8'), which is assumed to play a central role in stabilization of the active-site loop during complex formation. ATSI was immediately inactivated by pepsin and hardly represents an antinutritional component in foods or feeds.

Local breathing and global unfolding in hydrogen exchange of barnase and its relationship to protein folding pathways

We have measured the rate constants for exchange of amide protons in 15N-labeled wild-type barnase and a disulfide mutant that is more stable by 2 kcal.mol-1. The relative rate constants for exchange for wild type and mutant should reflect the changes in the equilibrium constants for local or global unfolding. The values for regions whose structure has been shown to be unaffected by the mutation fall into three subsets: those that are essentially unaffected by the mutation and so presumably exchange by local breathing; those where the energies change by close to 2 kcal.mol-1 and so presumably require global unfolding for exchange; and intermediate values that probably reflect a mixture of local and global unfolding in wild-type barnase. Amide protons that require the full change in unfolding energy are predominantly in the beta-sheet, which forms early in folding, but also include two that are involved in tertiary interactions that are known not to be formed until late in the folding pathway. Exchange in the major helix, which is known to form early, is largely unaffected by mutation and so exchanges by local breathing. There is thus no direct relationship between hydrogen-exchange behavior and the protein folding pathway. However, experiments on mutants of varying stability may provide further evidence on the sequence of events in folding.

13C NMR study of the effects of mutation on the tryptophan dynamics in chymotrypsin inhibitor 2: correlations with structure and stability

Recombinant chymotrypsin inhibitor 2 (CI-2) and the three mutants Ile39-->Val, Ile39-->Leu, and Arg67-->Ala were successfully enriched with [2-13C]tryptophan at position 24 within the hydrophobic core of the protein. Carbon-13 NMR relaxation measurements were then used to investigate the effect of these mutations on the dynamics of the tryptophan residue. In addition, the stability of wild-type and mutant CI-2s was measured by their susceptibility to unfolding by guanidine hydrochloride. The mutant proteins were all found to be less stable, giving delta delta GU values relative to wild-type of 1.17, 1.96, and 1.21 kcal mol-1, respectively. The indole moiety of the tryptophan residue was found to be more mobile in all the mutants studied than in wild-type CI-2. Order parameters of 0.69, 0.60, 0.56, and 0.44 were derived for wild-type, Ile39-->Val, Ile39-->Leu, and Arg67-->Ala CI-2, respectively. It is concluded that there is a correlation between the protein stability and the picosecond dynamics within the hydrophobic core and that mutations can influence the dynamic behavior of the residues that are relatively distant in the three-dimensional structure.

Natural protein proteinase inhibitors and their interaction with proteinases

The substrate-like 'canonical' inhibition by the 'small' serine proteinase inhibitors and the product-like inhibition by the carboxypeptidase inhibitor have provided the only atomic models of protein inhibitor--proteinase interactions for about 15 years. The recently published structures of cystatin/stefin--papain complexes and of hirudin--thrombin complexes reveal novel non-substrate-like interactions. In addition, the structure of pro-carboxypeptidase shows a model of inactivation which bears resemblance to proteinase/protein inhibitor systems. Considerable progress in understanding the transition between native and cleaved states of the serpins has also been made by several recent structural studies.

Mutations Pro----Ala-35 and Tyr----Phe-75 of Rhodobacter capsulatus ferrocytochrome c2 affect protein backbone dynamics: measurements of individual amide proton exchange rate constants by 1H-15N HMQC spectroscopy

Comparisons of hydrogen-deuterium solvent exchange rate constants for the NH protons of wild-type Pro----Ala-35 (P35A) and Tyr----Phe-75 (Y75F) Rhodobacter capsulatus ferrocytochromes c2 were made by 1H-15N heteronuclear multiple-quantum correlation spectroscopy. Exchange rate constants increased for the NH protons of residues 45-46, 54, 57-58, 60-61, 82-87, 98, and 100 with Y75F and 16-18, 20, 34, 37, 43, 45-46, and 58 with P35A. The increases in exchange rate constants are consistent with changes in unfolding equilibria and protein dynamics. In Y75F the exchange rate constants of the observable NH protons of the helix spanning Pro-79-Asp-89, namely Phe-82-Leu-87, increase to a similar degree, suggesting that this helix is a single cooperative unfolding unit compatible with the local unfolding model. As the oxidation-reduction potential of Y75F is 59 mV lower than wild-type cytochrome c2 (367 mV), the dynamic changes in this mutant, compared to wild-type, are proposed to be important determinants of the oxidation-reduction potential. Several differences between wild-type and Y75F are in common with P35A, a mutation which does not affect the oxidation-reduction potential, implying that not all observed dynamic changes are functionally important.

Design of a small peptide-based proteinase inhibitor by modeling the active-site region of barley chymotrypsin inhibitor 2

A synthetic peptide-based proteinase inhibitor was constructed by modeling the regions responsible for inhibition in barley chymotrypsin inhibitor 2 (CI-2). The 18-residue peptide was designed by molecular modeling, based on the crystal structure of CI-2. The amino acid sequences that interact with the proteinase were preserved, as well as residues that maintain the structure of the inhibitory loop. A disulfide bridge was introduced to force the peptide to adopt a cyclic structure. Kinetic studies on binding of the cyclic peptide to subtilisin BPN', subtilisin Carlsberg, chymotrypsin, and pancreatic elastase show that the cyclic peptide retains both the inhibition properties, the kinetic mechanism, and the specificity of the original protein inhibitor. Formation of a cyclic structure was found to be essential, and activity was abolished by reduction of the disulfide. As with CI-2, tightest binding is found to subtilisin BPN', where the Ki value for the cyclic peptide was 28 x 10(-12) M, compared with 29 x 10(-12)M for CI-2 under identical conditions. This remarkable result shows that it is possible to use a short synthetic peptide to model the molecular recognition properties of the intact protein, in this case obtaining full functionality with just 18 residues instead of 83 for CI-2.

Alternating zinc fingers in the human male associated protein ZFY: 2D NMR structure of an even finger and implications for "jumping-linker" DNA recognition

ZFY, a sex-related Zn-finger protein encoded by the human Y chromosome, is distinguished from the general class of Zn-finger proteins by the presence of a two-finger repeat. Whereas odd-numbered domains and linkers fit a general consensus, even-numbered domains and linkers exhibit systematic differences. Because this alternation may have fundamental implications for the mechanism of protein-DNA recognition, we have undertaken biochemical and structural studies of fragments of ZFY. We describe here the solution structure of a representative nonconsensus (even-numbered) Zn finger based on 2D NMR studies of a 30-residue peptide. Structural modeling by distance geometry and simulated annealing (DG/SA) demonstrates that this peptide folds as a miniglobular domain containing a C-terminal beta--hairpin and N-terminal alpha-helix (beta beta alpha motif). These features are similar to (but not identical with) those previously described in consensus-type Zn fingers (derived from ADR1 and Xfin); the similarities suggest that even and odd ZFY domains bind DNA by a common mechanism. A model of the protein-DNA complex (designated the "jumping-linker" model) is presented and discussed in terms of the ZFY two-finger repeat. In this model every other linker is proposed to cross the minor groove by means of a putative finger/linker submotif HX4HX3-hydrophobic residue-X3. Analogous use of a hydrophobic residue in a linker that spans the minor groove has recently been described in crystallographic and 3D NMR studies of homeodomain-DNA complexes. The proposed model of ZFY is supported in part by the hydroxyl radical footprint of the TFIIIA-DNA complex [Churchill, M.E.A., Tullius, T.D., & Klug, A. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 5528-5532].