Severe allergic conjunctivitis and chemosis caused by disodium cromoglycate

A 63-year-old man with chronic, nonallergic rhinoconjunctivitis presented immediate adverse reactions, such as intense itching, burning, redness and severe swelling of both conjunctivae after using disodium cromoglycate eye drops. Skin prick tests and conjunctival provocation tests were positive with pure disodium cromoglycate. Circulating IgE-specific antibodies to disodium cromoglycate in serum were demonstrated by RAST. We suggest that the acute ocular reaction was caused by disodium cromoglycate and that the underlying mechanism was probably an IgE-mediated immunological reaction.

C-capping and helix stability: the Pro C-capping motif

Here we have performed a statistical analysis of the protein database to find new putative local C-terminal motifs in alpha-helices. Our analysis shows that certain combinations of X-Pro pairs (Asn, Cys, His, Phe, Tyr, Trp, Ile, Val and Leu), in which residue X is the C-cap and the Pro is at position C', are more abundant than expected. In those pairs, except for the aliphatic residues, the presence of the Pro residue at C' tends to restrict the phi and psi dihedral angles of the residue at position C-cap, around -130 degrees , 70 degrees , respectively. For the aromatic residues as well as for His, the chi1 angle is around -60 degrees and the edge of the His and aromatic rings are close to the carbonyl group of the residue i - 4. In all the pairs having the above dihedral angles for residue C-cap, the main-chain amino group of Pro at C' is close to the last three main-chain carbonyls of the alpha-helix. The above structural arrangements suggests the existence of a stabilising electrostatic interaction of the residues at positions C-cap and C' with the helix macrodipole. We have denominated this putative local motif, the Pro-capping motif. To asses its importance in helix stability we have analysed by nuclear magnetic resonance (NMR) and far-UV circular dichroism (CD) a set of polyalanine-based peptides containing two of the above pairs: His-Pro and Phe-Pro, as well as the corresponding controls. In the case of the His-Pro pair we have found NMR evidence for the formation of the Pro-capping motif in aqueous solution. CD analysis shows that the presence of a Pro residue alters the C-cap properties of the preceding amino acids in the case of His and Phe makes them more favourable. The Pro-capping motif with the appropriate sequence, determines the location of the C terminus of alpha-helices and stabilises the helical conformation having Pro as the C' residue.

The photochemical reflectance index: an optical indicator of photosynthetic radiation use efficiency across species, functional types, and nutrient levels

The photochemical reflectance index (PRI), derived from narrow-band reflectance at 531 and 570 nm, was explored as an indicator of photosynthetic radiation use efficiency for 20 species representing three functional types: annual, deciduous perennial, and evergreen perennial. Across species, top-canopy leaves in full sun at midday exhibited a strong correlation between PRI and ΔF/Fm', a fluorescence-based index of photosystem II (PSII) photochemical efficiency. PRI was also significantly correlated with both net CO₂ uptake and radiation use efficiency measured by gas exchange. When species were examined by functional type, evergreens exhibited significantly reduced midday photosynthetic rates relative to annual and deciduous species. This midday reduction was associated with reduced radiation use efficiency, detectable as reduced net CO₂ uptake, PRI, and ΔF/Fm' values, and increased levels of the photoprotective xanthophyll cycle pigment zeaxanthin. For each functional type, nutrient deficiency led to reductions in both PRI and ΔF/Fm' relative to fertilized controls. Laboratory experiments exposing leaves to diurnal courses of radiation and simulated midday stomatal closure demonstrated that PRI changed rapidly with both irradiance and leaf physiological state. In these studies, PRI was closely correlated with both ΔF/Fm' and radiation use efficiency determined from gas exchange at all but the lowest light levels. Examination of the difference spectra upon exposure to increasing light levels revealed that the 531 nm Δ reflectance signal was composed of two spectral components. At low irradiance, this signal was dominated by a 545-nm component, which was not closely related to radiation use efficiency. At progressively higher light levels above 100 μmol m^-2 s^-1, the 531-nm signal was increasingly dominated by a 526-nm component, which was correlated with light use efficiency and with the conversion of the xanthophyll pigment violaxanthin to antheraxanthin and zeaxanthin. Further consideration of the two components composing the 531-nm signal could lead to an index of photosynthetic function applicable over a wide range of illumination. The results of this study support the use of PRI as an interspecific index of photosynthetic radiation use efficiency for leaves and canopies in full sun, but not across wide ranges in illumination from deep shade to full sun. The discovery of a consistent relationship between PRI and photosynthetic radiation use efficiency for top-canopy leaves across species, functional types, and nutrient treatments suggests that relative photosynthetic rates could be derived with the "view from above" provided by remote reflectance measurements if issues of canopy and stand structure can be resolved.

Role of beta-turn residues in beta-hairpin formation and stability in designed peptides

The sequence RGITVNGKTYGR has been reported as part of a de novo design peptide system. This peptide folds as a beta-hairpin structure with three residues per strand and two residue turns. Asn6 side-chain, the residue in position L1 of the beta-turn, appeared to be solvent exposed, interacting only within the turn but not with the rest of the peptide. We have chosen this position as a good candidate to design mutations, based on the protein database statistical abundances, that should mainly affect the turn stability and possibly the pairing between strands. We have found that all NMR parameters, in particular the conformational shift analysis of CalphaH and the coupling constants, 3JHNalpha, correlate very well and show similar conformational features in all the turn mutant peptides. The population estimates are in reasonable agreement among the different methods used. It appears that the peptide with Asn in position L1 is the most structured peptide, followed by the one with Asp6. The next structured peptide is the one with Gly6. The least populated peptides were those with Ala6 and Ser6. We have found a strong correlation between the hairpin population, as determined from the conformational shift of CalphaH and the occurrence of the different residues at position L1 of beta-hairpins with type I' beta-turn, in the protein database. Our analysis demonstrates that this peptide system is sensitive enough to register small energy changes in the hairpin structure; therefore, it constitutes an appropriate model to quantify energy contributions, once the appropriate sheet/coil transition algorithm is developed. Comparison with the other studies indicate that the design of a specific hairpin structure must involve a sequence at the turn region favouring the desired turn type, and a sequence at the strands that avoids alternative interstrand side-chain pairings.

Loop length, intramolecular diffusion and protein folding

Intramolecular diffusion plays a role in protein folding as shown by kinetic experiments on two alpha-spectrin SH3 domain circular permutants (S19-P20s and N47-D48s), with different poly-glycine loop lengths. Insertion of up to 10 Gly residues does not alter the structure of the folded state nor the overall characteristics of the denatured ensemble. The apparent level of the energy barrier between the denatured and folded species increases linearly with the number of inserted glycines. This suggests that the transition state itself and/or possibly previous transient unstable intermediates are accessed with more difficulty when loop length is increased. The fact that the induced impediment is directly proportional to the number of Gly residues and not to the free energy difference in the folded state indicates that diffusion of different parts of the molecule relative to each other is taking place on going from the denatured ensemble to the transition state. Our results also suggest that transition state ensembles could be more homogenous than recently postulated.

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.

In vitro induction of micronuclei in lymphocytes: the use of bromodeoxyuridine as a proliferation marker

A simple method to determine the induction of micronuclei in cultured lymphocytes is described as an alternative to the cytochalasin-B method. It is proposed for use in the evaluation of the genotoxic potential of agents in vitro. It allows the recording of events only in the proliferating population of cells and at the same time it eliminates the possibility of recording combined effects with a cytokinesis-blocking agent. 16 microM bromodeoxyuridine (BrdU) was used to label proliferating cells that were treated with colcemid or mitomycin C at different concentrations. A monoclonal antibody against BrdU incorporated in the DNA and a peroxidase-diaminobenzidine brown stain were used to identify those cycling cells in a slide. To obtain the maximum yield of micronuclei, the best time for the addition of bromodeoxyuridine was found to be at 40 h from the initiation of cultures, 8 h before treating cells with the chemicals. Identification of micronuclei was easy, fast and unequivocal. In addition, the formation of structures similar to micronuclei, but that still are part of the nucleus could be observed. It is not clear if these structures are an intermediate stage in the formation of MN, but this methodology provides the possibility of observing and studying them.

1H and 15N NMR assignment and solution structure of the SH3 domain of spectrin: comparison of unrefined and refined structure sets with the crystal structure

The assignment of the 1H and 15N nuclear magnetic resonance spectra of the Src-homology region 3 domain of chicken brain alpha-spectrin has been obtained. A set of solution structures has been determined from distance and dihedral angle restraints, which provide a reasonable representation of the protein structure in solution, as evaluated by a principal component analysis of the global pairwise root-mean-square deviation (rmsd) in a large set of structures consisting of the refined and unrefined solution structures and the crystal structure. The solution structure is well defined, with a lower degree of convergence between the structures in the loop regions than in the secondary structure elements. The average pairwise rmsd between the 15 refined solution structures is 0.71 +/- 0.13 A for the backbone atoms and 1.43 +/- 0.14 A for all heavy atoms. The solution structure is basically the same as the crystal structure. The average rmsd between the 15 refined solution structures and the crystal structure is 0.76 A for the backbone atoms and 1.45 +/- 0.09 A for all heavy atoms. There are, however, small differences probably caused by intermolecular contacts in the crystal structure.

Non-native local interactions in protein folding and stability: introducing a helical tendency in the all beta-sheet alpha-spectrin SH3 domain

The relative importance of secondary structure interactions versus tertiary interactions for stabilising and guiding the folding process is a matter for discussion. Phenomenological models of protein folding assign an important role to local contacts in protein folding and stability. On the other hand, simplistic lattice simulations find that secondary structure is mainly the product of protein compaction and that optimisation of folding speed seems to require small contributions of local contacts to the stability of the folded state. To examine the extent to which secondary structure propensities influence protein folding and stability, we have designed mutations that introduce a strong non-native helical propensity in the first 19 residues of the alpha-spectrin SH3 domain. The mutant proteins have the same three-dimensional structure as the wild-type, but they are less stable and have less co-operative folding transitions. There seems to be a relationship between the non-native helical propensity and the compaction of the denatured state. This suggests that in the denatured ensemble under native conditions there is a significant proportion of compact structures with non-native secondary structures. Our results demonstrate that non-local interactions can overcome strong non-native secondary structure propensities and, more important, that optimisation of folding speed and co-operativity requires the latter to be relatively small.

Apoptosis and proliferation of fibroblasts during postnatal skin development and scleroderma in the tight-skin mouse

Tight-skin (Tsk) is a dominant gene mutation that causes a fibrotic skin disease in mice, similar to human scleroderma. Both conditions are characterized by increased numbers of dermal fibroblasts containing high levels of procollagen mRNA. Whether this fibroblast population arises from fibroblast growth or fibroblast transcriptional activation is debated. Proliferation and apoptosis of fibroblasts of normal and Tsk mice were studied in skin sections before, at onset, and in established fibrosis. Tissues sections were immunostained with proliferating cell nuclear antigen (PCNA) as proliferation marker. Apoptosis was investigated by in situ end-labeling of fragmented DNA and nuclear staining with propidium iodide. The expression of the apoptosis inhibitor Bcl-2 was investigated by immunohistochemistry. We demonstrate differences in fibroblast proliferation and apoptosis related to postnatal skin growth and development. Neonatal skin exhibits the highest levels of proliferation and apoptosis in fibroblasts. In contrast, low proliferation and absence of apoptosis characterizes adult fibroblasts. Skin fibroblasts express Bcl-2 only in newborns, and at other ages Bcl-2 was restricted to epithelial cells. Our results also suggest that neither increased fibroblast proliferation nor defective apoptosis accounts for the fibrotic phenotype of Tsk. Therefore, transcriptional activation of extracellular matrix genes appears more relevant in the pathogenesis of Tsk fibrosis.

Development of the multiple sequence approximation within the AGADIR model of alpha-helix formation: comparison with Zimm-Bragg and Lifson-Roig formalisms

In this work we present the development of the multiple sequence approximation (AGADIRms) and the standard one-sequence approximation (AGADIRls) within the framework of AGADIR's alpha-helix formation model. The extensive comparison between these new formulations and the original one [AGADIR; V. Muñoz and L. Serrano (1994). Nat. Struct. Biol., Vol. 1, pp. 399-409] indicates that the standard one-sequence approximation is virtually identical to the multiple sequence approximation, while the previously used residue partition function approximation [Muñoz and Serrano (1994); (1995), J. Mol. Biol., Vol. 245, pp. 275-296] is less precise. The calculations of the average helical content performed with AGADIR are precise for peptides of less than 30 residues and progressively diverge from the multiple sequence formulation for longer peptides. The helicity distribution of heteropolypeptides with less than 50% average helical content is also well described, while those of quasi-homopolymers with high helical content tend to be-flattened. These inaccuracies lead to an underestimation of 0.017 kcal/mol for the mean-residue enthalpic contribution in AGADIR, as compared to AGADIRms and AGADIRls. The other energy contributions to alpha-helix stability are not affected by the original statistical approximation. We also discuss the particularities of the model for alpha-helix formation utilized in AGADIR and compare it with the classical Zimm-Bragg and Lifson-Roig theories. Moreover, we develop the mathematical relationships between the basic AGADIR energy contributions and helix nucleation and elongation, which permit the quantitative comparison between formalisms. Remarkably, the comparison between AGADIRms and the Lifson-Roig formalism shows that, despite the differences on treating helix/coil cooperativity, both theories give virtually identical results when an equivalent set of parameters is used. This indicates that the helix/coil transition is a solid theory independent of the particularities of the model for alpha-helix formation.

Folding kinetics of Che Y mutants with enhanced native alpha-helix propensities

In this work we study the folding kinetics of Che Y mutants in which the helical propensity of each of its five alpha-helices has been greatly enhanced by local interactions (between residues close in sequence). This constitutes an experimental test on the role of local interactions in protein folding, as well as providing new information on the details of the folding pathway of the protein Che Y. With respect to the first issue, our results show that the enhancement of helical propensities by native-like local interactions in Che Y has the following general effects: (1) the energetics of the whole Che Y folding energy landscape (folded state, intermediate, denatured state and main transition state) are affected by the enhancement of helical propensities, thus, native-like local interactions appear to have a low specificity for the native conformation; (2) our results support the idea, proposed from thermodynamic analysis of the mutants, that the denatured state under native conditions becomes more compact upon enhancement of helical propensities; (3) the rate of folding in aqueous solution decreases in all the mutants, suggesting that the optimization of the folding rate in this protein requires low secondary structure propensities. Regarding the description of the folding pathway of Che Y, we find evidence that the folding transition state of Che Y is constituted by two sub-domains with different degree of helical structure. The first includes helices 1 and 2 which are rather structured, while the second encompasses the last three helices, which are very unstructured. On the other hand, the same analysis for the folding intermediate indicates that all the five alpha-helices are, on average, rather structured. Thus, suggesting that a large structural reorganization of the last three alpha-helices must take place before folding can be completed. This conclusion indicates that the folding intermediate of Che Y is a misfolded species.

Diagnostic and therapeutic thoracoscopy in esophageal cancer

The decision before operation whether an esophagus affected by cancer can be resected is difficult. In order to determine if the tumor can be removed or not, patients must undergo surgery. This high risk intervention is often carried out only to prescribe palliative treatment. We used a thoracoscopic technique for the diagnosis and resection of esophageal cancer with the aim of improving the high morbidity rate associated with esophageal open surgery. A right thoracoscopy was performed in seven patients and only four underwent resection. The entire esophagus was mobilized thoracoscopically and the intervention was completed through the abdomen and the neck. In three patients in whom resection was not considered possible, the thoracoscopic procedure was done with excellent tolerance, and treated by palliative methods. Thoracoscopy is a very valuable procedure for the diagnosis of resectability as well as for the mobilization of the esophagus prior to resection.

Characterisation of the isolated Che Y C-terminal fragment (79-129)--Exploring the structure/stability/folding relationship of the alpha/beta parallel protein Che Y

To gain insight into how the three-dimensional structure, stability and folding of the protein Che Y are related to one another, we have performed a conformational analysis of a long fragment of this protein, encompassing its C-terminal 51 residues (79-129). This fragment consists of residues in the beta-strands 4 and 5 and alpha-helices 4 and 5 of native Che Y. The study has been performed by two-dimensional NMR and far-ultraviolet circular dichroism in aqueous solution and in 30% (by vol.) trifluoroethanol/ water at 273 K and 298 K. We observe little structure for this fragment in aqueous solution which could be due to low helical populations in the regions corresponding to helices 4 and 5. Within the limits of the residual helical structure experimentally detected, helix 4 appears to extend beyond the N-terminus observed in the native structure by over four residues belonging to the preceding loop. In 30% trifluoroethanol the helical content of both helices increase and helix 4 extends further to include the preceding beta-strand 4. None of the long-range NOEs present in native Che Y are observed under the explored experimental conditions. The conformational shifts of the H(alpha) protons within the alpha-helices of fragment 79-129 are identical to those of shorter synthetic peptides corresponding to the isolated alpha-helices. Thus, the fragment 79-129 appears to behave as an open chain with low local helical populations. The very low intrinsic ability for structure formation displayed by this region of Che Y at pH 2.5 suggests that in the folded protein this region could be mainly stabilised by interactions with the N-terminal Che Y region. This is in accordance with the contact map of Che Y, which shows that the strongest non-local contacts of C-terminal residues are with residues of the N-terminal region, while those within the C-terminal region are very weak. More importantly, the relationship appears to be possibly extended to the folding properties of the protein, since the C-terminal region is not structurally formed in the folding transition state of Che Y but in the final steps of the folding.

Favourable native-like helical local interactions can accelerate protein folding

BACKGROUND

Extensive studies of peptide conformation have provided reasonable knowledge of the rules determining helix stability. This knowledge can be used to stabilize proteins against chemical and thermal denaturation. This has been done in two proteins: the chemotactic protein from Escherichia coli, Che Y (a 129 aa alpha/beta parallel protein with five alpha-helices, which shows an accumulating intermediate during refolding) and the activation domain of human procarboxypeptidase A2, ADA2h (a 81 aa alpha + beta protein domain, with two alpha-helices, which follows a two-state mechanism). As the introduced stabilizing interactions are local in nature, the energy balance between the contribution of local and nonlocal interactions changes considerably. Recent theoretical analyses of protein folding using simplified models have indicated that optimization of folding speed requires this balance to be biased towards nonlocal interactions. To determine whether this is the case, we study here the folding kinetics of two ADA2h mutants in which alpha-helix 1 (mutant M1) or 2 (mutant M2) has been stabilized through local interactions, as well as the equilibrium and kinetic behaviour of a double mutant (DM) in which both helices have been stabilized.

RESULTS

The stability of DM is considerably enhanced with respect to wild type (WI) and this mutant can be considered as a thermoresistant protein (Tm > 363 K). The thermodynamic parameters obtained by chemical denaturation (urea and GdnHCl) show that DM is approximately 2.6 kcal mol-1 more stable than WT. The effects on folding kinetics are different in each of the single mutants. M1 shows very little effect in refolding, while its unfolding is greatly decelerated with respect to WT. M2 shows, together with a deceleration in unfolding, a significant acceleration in refolding. As with equilibrium parameters, the kinetics of the double mutant can be explained by the simple addition of the effects found in each single mutant. Interestingly enough, the refolding slope mkf in mutants M2 and DM is smaller than in the wild-type and M1 mutant.

CONCLUSIONS

Thermoresistance can be achieved, in some cases, by increasing favourable native local interactions. The balance between local and nonlocal interactions can be significantly changed in some proteins and still keep a cooperative unfolding transition similar to that of the wild type. The introduction of favourable local interactions by mutational redesign can also be used to increase the folding speed of certain proteins, showing that not all proteins in nature have been optimized for rapid folding, contrary to what has been theoretically indicated. This behaviour is probably also shared by other polypeptides with highly unstructured denatured states. All these phenomena have been shown experimentally in ADA2h by mutations that increase helix stability. However, the effects promoted for such an approach in proteins with residual structure and/or intermediates in the denatured ensemble could be different. This has been shown by experiments performed on CheY in which the cooperativity of the folding process was greatly affected.

Conformational analysis of peptides corresponding to all the secondary structure elements of protein L B1 domain: secondary structure propensities are not conserved in proteins with the same fold

The solution conformation of three peptides corresponding to the two beta-hairpins and the alpha-helix of the protein L B1 domain have been analyzed by circular dichroism (CD) and nuclear magnetic resonance spectroscopy (NMR). In aqueous solution, the three peptides show low populations of native and non-native locally folded structures, but no well-defined hairpin or helix structures are formed. In 30% aqueous trifluoroethanol (TFE), the peptide corresponding to the alpha-helix adopts a high populated helical conformation three residues longer than in the protein. The hairpin peptides aggregate in TFE, and no significant conformational change occurs in the NMR observable fraction of molecules. These results indicate that the helical peptide has a significant intrinsic tendency to adopt its native structure and that the hairpin sequences seem to be selected as non-helical. This suggests that these sequences favor the structure finally attained in the protein, but the contribution of the local interactions alone is not enough to drive the formation of a detectable population of native secondary structures. This pattern of secondary structure tendencies is different to those observed in two structurally related proteins: ubiquitin and the protein G B1 domain. The only common feature is a certain propensity of the helical segments to form the native structure. These results indicate that for a protein to fold, there is no need for large native-like secondary structure propensities, although a minimum tendency to avoid non-native structures and to favor native ones could be required.

Role of a nonnative interaction in the folding of the protein G B1 domain as inferred from the conformational analysis of the alpha-helix fragment

BACKGROUND

The role of local interactions in protein folding and stability can be investigated by the conformational analysis of protein fragments. The hydrophobic staple and Schellman motifs have been described at the N and C terminus, respectively, of protein alpha-helices. These motifs are characterized by an interaction between two hydrophobic residues, one outside the helix and one within the helix, and their importance for helix stability has been analyzed in model peptides. In the alpha-helix of the protein G B1 domain, only the Schellman motif is formed--the hydrophobic staple motif is absent despite the favourable sequence pattern. We have experimentally analyzed the solution conformation of the 19-41 fragment of protein G. This peptide comprises the helical residues and contains both the hydrophobic staple and Schellman motif sequences.

RESULTS

In the isolated peptide in water, the hydrophobic staple motif is formed and stabilizes the helical structure as compared with a shorter peptide lacking it, but the Schellman motif is not formed. In 30% aqueous TFE, the helix is more stable than in pure water and both motifs are formed.

CONCLUSIONS

The results suggest that the importance of each motif for the folding and stability of protein G is different. The nonnative hydrophobic staple interaction can help to nucleate the helix at the beginning of folding but has later to be disrupted. The Schellman motif, while not providing enough energy for substantial helix stabilization in the unfolded state, could be important for determining the local fold of the sequence in the context of the rest of the protein.

Different folding transition states may result in the same native structure

The crystal structures of two circular permutants of the alpha-spectrin SH3 domain with new termini within the RT loop (S19-P20s) and the distal loop (N47-D48s) have been determined at 2.02 and 1.77 A resolution respectively. Both fold into the same three-dimensional structure as the wild-type SH3 domain except for the engineered loop that fuses the wild-type termini. The cleaved RT loop in S19-P20s loses nine conserved hydrogen bonds through local hydrogen bond unzipping; no hydrogen bond unzipping occurs in N47-D48s. The structures of the transition states for folding of wild-type alpha-spectrin SH3 domain and the two circular permutants have been examined by analysis of the folding kinetics of eight strategically distributed point mutants. Unlike the native structures, the transition states of the three proteins are considerably different, suggesting that there is no direct relationship between these two states in a protein.

Rational design of specific high-affinity peptide ligands for the Abl-SH3 domain

SH3 domains bind proline-rich peptides with affinities in the order of 0.2-50 microM. In general, these domains are quite promiscuous, and the same peptide can bind to several different SH3 domains with similar affinities (i.e., 3BP1 peptide to Abl- and Fyn-SH3). This poor affinity and specificity make it difficult to elucidate their role in vivo as well as the use of peptides to specifically bind to a single domain. Here, we report that by using existing biocomputing tools, as well as simple physicochemical reasoning, it is possible to design mutations in the 3BP1 peptide (Met4-Tyr, Pro5-Ser, and Leu8-Pro), so that the affinity for Abl-SH3 increases 20-fold (p40 peptide: APTYSPPPPP; Kd = 0.4 microM), while that for the closely related domain, Fyn-SH3, decreases 10-fold. Both the RT and n-Src loops are responsible for regulating the specificity for Pro-rich ligands and more specifically residues Ser15, Thr19, and Glu38 in Abl-SH3. The first six positions in the 3BP1 peptide are important for determining the specificity for SH3 domains, while the remaining four seem to be more important for the affinity. Moreover, by choosing rationally the substituents, it is possible to replace some of the Pro residues postulated to be essential for the interaction with SH3 domains and still have a significant affinity. This indicates that the sequence repertoire that could interact with a specific SH3 domain could be larger than previously thought.

De novo design and structural analysis of a model beta-hairpin peptide system

We have designed de novo a simple, context-free, model linear peptide system to fold into a regular beta-hairpin structure, with three-residue beta-strands connected by a type I' beta-turn. CD and NMR analysis of this peptide in aqueous solution show that the peptide folds into the expected conformation. Structural characterization of three peptide variants in which some of the strand side-chains have been substituted by alanine, demonstrates that inter-strand side chain-side chain interactions are essential for beta-hairpin formation. This simple model system will help to isolate the factors behind beta-sheet formation, and contribute useful information about de novo protein design.

Infrared evidence of a beta-hairpin peptide structure in solution

The IR spectrum of an 16-amino acid peptide corresponding, according to NMR studies, to a beta-hairpin has been analysed. Two characteristic features distinguish its spectrum from that of an antiparallel beta-sheet: the low-frequency band that in a beta-sheet structure is located at approximately 1632 cm-1 appears here at approximately 1620 cm-1, and the high-frequency component does not undergo the isotopic shift typical of beta-sheet from 1690 to 1675 cm-1 when transferred to D2O. The infrared characteristics associated with beta-hairpins have been described so far in two proteins, in one of which, whose three-dimensional structure is known from X-ray diffraction, a beta-hairpin has actually been detected.

The three-dimensional structure of two mutants of the signal transduction protein CheY suggest its molecular activation mechanism

The three-dimensional crystal structures of the single mutant M17G and the triple mutant F14G-S15G-M17G of the response regulator protein CheY have been determined to 2.3 and 1.9 angstrom, respectively. Both mutants bind the essential Mg2+ cation as determined by the changes in stability, but binding does not cause the intrinsic fluorescence quenching of W58 observed in the wild-type protein. The loop beta4-alpha4 appears to be very flexible in both mutants and helix alpha4, which starts at N94 in the native Mg2+-CheY and at K91 in the native apo-CheY, starts in both mutants at residue K92. The side-chain of K109 appears to be more mobile because of the space freed by the M17G mutation. In the triple mutant the main chain of K109 and adjacent residues (loop beta5-alpha5) is displaced almost by 2 angstrom affecting the main chain at residues T87 to E89 (C terminus of beta4). The triple mutant structure has a Mg2+ bound at the active site, but although the Mg2+ coordination is similar to that of the native Mg2+-CheY, the structural consequences of the metal binding are quite different. It seems that the mutations have disrupted the mechanism of movement transmission observed in the native protein. We suggest that the side-chain of K109, packed between V86, A88 and M17 in the native protein, slides forwards and backwards upon activation and deactivation dragging the main chain at the loop beta5-alpha5 and triggering larger movements at the functional surface of the protein.