Introduction of a new method for measuring young children’s mental health at child health clinics

The Child Healthcare Services (CHS) in Sweden offer regular health check-ups and reach almost all 0-5-year-old children. Parents of all children aged 3 to 5 are invited for a free check-up around their child birthday. Although one of the objectives of the CHS is to detect mental health problems, evidence-based methods are not used for this purpose at the Child Health Clinics (CHC). Therefore, we assumed that introduction of a new instrument (the Strengths and Difficulties Questionnaire - SDQ) to assess children's emotional and behavioural problems through parent and teacher reports, would not only help to test the hypotheses in our population-based trail (Children and Parents in Focus), but it would also address CHC's needs to detect children's mental health problems.

Three months into the study, we realised that a lower than expected number of SDQs were returned by parents and teachers. We started exploring the problem through individual interviews with nurses, parents and preschool teachers. Results showed that nurses found it useful for their assessment to have access to preschool teachers' SDQ-ratings. Parents were also positive to the procedure but had concerns regarding confidentiality of the responses. Preschool teachers were least positive, fearing labelling of children and negative parental reactions. We used a range of facilitation strategies such as educational meetings, outreach visits and newsletter to support nurses in implementation of the new procedure. To address parental concerns, we removed some of the questions and redesigned the questionnaires. This resulted to an overall increase of 10-15% in the response rate.

The findings suggest that implementing the SDQ at CHCs to assess the mental health of 3-5-year-olds is feasible, but reaching all children remains a challenge that requires more attention.

Strengths and Difficulties Questionnaire (SDQ) as an assessment tool for measuring emotional and behavioural problems in young children

Evaluation of new initiatives to tackle mental health problems in children requires instruments that are both valid and reliable. One such instrument is the Strengths and Difficulties Questionnaire (SDQ), an assessment tool for child emotional and behavioural problems. The instrument was developed by Goodman in the 1990's and is being used worldwide in both clinical settings and research projects.

However, previous studies on the SDQ have mainly focused on school-aged children and adolescents. We know very little about the usefulness of the SDQ for measuring preschool children's mental health problems. Using data from a large number of parents and preschool teachers of children aged 3-5 (> 11 000 questionnaires), we tested the psychometric properties of the SDQ, examined the inter-rater agreement and provided cut-off points.

The original five-factor model of the SDQ was supported and it was shown to be a reliable instrument in the hands of mothers, fathers and preschool teachers. We also found significant, albeit poor, agreement (ICC) between parent and teacher ratings and good agreement between parents' ratings. Teachers reported lower levels of problems compared to parents. Compared to girls, boys were generally reported to have more problems. Thus, we provided separate cut-offs for each age group, gender and rater category.

The results suggest that SDQ can reliably be used for measuring emotional and behavioural problems in young children in community settings. They also suggest that parent and teacher reports are complementary; hence, reports from both types of informants should be considered when using the SDQ as a method to identify mental health problems within the child health services. However, inter-rater agreement between mothers and fathers was good, meaning that it may be sufficient to obtain data from a single parent informant.

Nurses' experiences of screening for communication difficulties at 18 months of age

AIM

Early identification of communication disorders is important and may be possible through screening in the child health services. The aim of the study was to investigate nurses' experiences and sense of competence when using the Infant-Toddler Checklist (ITC) communication screening at the 18-month health visit.

METHODS

A mixed-methods design including three focus group interviews (n = 14) and a web-based survey (n = 22) among nurses using the ITC or the standard method. Interview data were analysed through systematic text condensation and a deductive analysis based on implementation theory. Groups were compared using Mann-Whitney tests.

RESULT

Three themes emerged: Using a structured evaluation of communication changes, the dynamic, ITC is a beneficial tool and Implementation of the ITC faces a few challenges. Nurses who used the ITC perceived to a greater extent that they used a structured method (p = 0.003, r = 0.9) and felt more secure in describing the child's communication and language development to parents (p = 0.006, r = 0.83) compared to the standard method group.

CONCLUSION

Using the ITC supported the nurses in their assessment of communication at 18 months. Nurses' sense of competence was higher when using the ITC, both in their assessment and in communicating with parents.

Field demonstration of mode-division multiplexing upgrade scenarios on commercial networks

We demonstrate three possible scenarios for upgrading current single-mode transmission networks with high capacity few-mode fiber technology using mode-division multiplexing (MDM). The results were obtained from measurements over a number of field-deployed single-mode fiber links with an additional experimental in-line amplified few-mode fiber link. The results confirm the viability of employing MDM using few-mode fiber technology to gradually replace legacy optical systems.

Mid-IR microspectroscopic imaging of breast tumor tissue sections

IR microspectroscopic imaging is a relatively new approach for the examination of tissue sections. In contrast to standard light microscopy based procedures, the IR approach requires neither sample staining nor fixation. The IR spectra of breast tumor tissue sections are obtained via a microscope equipped with a focal plane array detector. This enabled the simultaneous collection of individual mid-IR spectra from thousands of different sample positions with a spatial resolution near the diffraction limit. The analysis of the IR data reveals a high sensitivity of the IR approach toward changes in tissue biochemistry and variations in breast tissue architecture. Moreover, the data demonstrate the need for collecting spectra with high spatial resolution at the level of individual cells. This minimizes problems associated with tissue microheterogeneity and is an essential prerequisite for future studies aimed at developing IR microspectroscopic imaging as a complement to present diagnostic tools for breast cancer.

Study of the conformational transition of A beta(1-42) using D-amino acid replacement analogues

A critical event in Alzheimer's disease is the transition of Abeta peptides from their soluble forms into disease-associated beta-sheet-rich conformers. Structural analysis of a complete D-amino acid replacement set of Abeta(1-42) enabled us to localize in the full-length 42-mer peptide the region responsible for the conformational switch into a beta-sheet structure. Although NMR spectroscopy of trifluoroethanol-stabilized monomeric Abeta(1-42) delineated two separated helical domains, only the destabilization of helix I, comprising residues 11-24, caused a transition to a beta-sheet structure. This conformational alpha-to-beta switch was directly accompanied by an aggregation process leading to the formation of amyloid fibrils.

Conversion of yeast phosphoglycerate kinase into amyloid-like structure

Yeast phosphoglycerate kinase is a structurally well-characterized enzyme consisting of 415 amino acids without disulfide bonds. Anion-induced refolding from its acid-unfolded state gives rise to the formation of worm-like amyloid fibrils with a persistence length of 73 nm. Electron microscopy and small-angle X-ray scattering data indicate that the fibrils have an elliptical cross-section with dimensions of 10.2 nm x 5.1 nm. About half of all amino acids are organized in form of cross-beta structure which gives rise to typical infrared spectra, X-ray diffraction and yellow-green birefringence after Congo red staining. The kinetics of amyloid formation, monitored by infrared spectroscopy, dynamic light scattering and X-ray scattering, was found to be strongly dependent on protein concentration. The infrared data indicate that the formation of cross-beta structure practically comes to an end already after some hours, whereas the length-growth of the amyloid fibrils, monitored by small-angle X-ray scattering, was not yet completed after 1,300 hours.

Two-dimensional IR correlation spectroscopy: sequential events in the unfolding process of the lambda cro-V55C repressor protein

A question often posed in protein folding/unfolding studies is whether the process is fully cooperative or whether it contains sequential elements. To address this question, one needs tools capable of resolving different events. It seems that, at least in certain cases, two-dimensional (2D) IR correlation spectroscopy can provide answers to this question. To illustrate this point, we have turned to the Cro-V55C dimer of the lambda Cro repressor, a protein known to undergo thermal unfolding in two discrete steps through a stable equilibrium intermediate. The secondary structure of this intermediate is compatible with that of a partially unfolded protein and involves a reorganization of the N terminus, whereas the antiparallel beta-ribbon formed by the C-terminal part of each subunit remains largely intact. To establish whether the unfolding process involves sequential events, we have performed a 2D correlation analysis of IR spectra recorded over the temperature range of 20-95 degrees C. The 2D IR correlation analysis indeed provides evidence for a sequential formation of the stable intermediate, which is created in three (closely related) steps. A first step entails the unfolding of the short N-terminal beta-strand, followed by the unfolding of the alpha-helices in a second step, and the third step comprises the reorganization of the remaining beta-sheet and of some unordered segments in the protein. The complete unfolding of the stable intermediate at higher temperatures also undergoes sequential events that ultimately end with the breaking of the H bonds between the two beta-strands at the dimer interface.

Water-soluble beta-sheet models which self-assemble into fibrillar structures

Self-assembly of beta-sheet domains resulting in the formation of pathogenic, fibrillar protein aggregates (amyloids) is a characteristic feature of various medical disorders. These include neurodegenerative diseases, such as Alzheimer's, Huntington's, and Creutzfeldt-Jacob's. A significant problem in studying such aggregation processes is the poor solubility of these beta-sheet complexes. The present work describes water-soluble de novo beta-sheet peptides which self-assemble into fibrillar structures. The model peptides enable studies of the relationship between beta-sheet stability and association behavior. The peptides [DPKGDPKG-(VT)n-GKGDPKPD-NH2, n = 3-8] are composed of a central beta-sheet-forming domain (VT-sequence), and N- and C-terminal nonstructured octapeptide sequences which promote water solubility. Conformational analyses by circular dichroism and Fourier transform infrared spectroscopy indicate the influence of peptide length, D-amino acid substitution, and concentration on the ability of the peptides to form stable beta-sheet structures. The association behavior investigated by analytical ultracentrifugation and dynamic light scattering was found to correlate strongly with the stability of a beta-sheet conformation. Model peptides with n >/= 6 form stable, water-soluble beta-sheet complexes with molecular masses of more than 2000 kDa, which are organized in fibrillar structures. The fibrils examined by Congo Red staining and electron microscopy show some similarities with naturally occurring amyloid fibrils.

Secondary structure and oligomerization behavior of equilibrium unfolding intermediates of the lambda cro repressor

The thermal unfolding of the wild-type Cro repressor, its disulfide-bridged mutant Cro-V55C (with the Val-55 --> Cys single amino acid substitution), and a CNBr-fragment (13-66)2 of Cro-V55C was studied by Fourier transform infrared spectroscopy and dynamic light scattering. The combined approach reveals that thermal denaturation of Cro-WT and Cro-V55C proceeds in two steps through equilibrium unfolding intermediates. The first thermal transition of the Cro-V55C dimer involves the melting of the alpha-helices and the short beta-strand localized in the N-terminal part of the molecule. This event is accompanied by the formation of tetramers, and also impacts on the hydrogen-bonding interactions of the C-terminal beta-strands. The beta-sheet formed by the C-terminal parts of each polypeptide chain is the major structural feature of the intermediate state of Cro-V55C and unfolds during a second thermal transition, which is accompanied by the dissociation of the tetramers. Cutting of 12 amino acids in the N-terminal region is sufficient to prevent the formation of alpha-helical structure in the CNBr-fragment of Cro-V55C, and to induce tetramerization already at room temperature. The tetramers may persist over a broad temperature range, and start to dissociate only upon thermal unfolding of the beta-sheet structure formed by the C-terminal regions. The wild-type protein is a dimer at room temperature and at protein concentrations of 1.8-5.8 mg/mL. At lower concentrations, the dimers are stable until the onset of thermal unfolding, which is accompanied by the dissociation of the dimers into monomers. At higher protein concentrations, the unfolding is more complex and involves the formation of tetramers at intermediate temperatures. At these intermediate temperatures, the Cro-WT has lost all of its alpha-helical structure and also most of its native beta-sheet structure. Upon further temperature increase, a tendency for an intermolecular association of the beta-strands is observed, which may result in irreversible beta-aggregation at high protein concentrations.

New structural insights into the refolding of ribonuclease T1 as seen by time-resolved Fourier-transform infrared spectroscopy

To get new structural insights into different phases of the renaturation of ribonuclease T1 (RNase T1), the refolding of the thermally unfolded protein was initiated by rapid temperature jumps and detected by time-resolved Fourier-transform infrared spectroscopy. The characteristic spectral changes monitoring the formation of secondary structure and tertiary contacts were followed on a time scale of 10(-3) to 10(3) seconds permitting the characterization of medium and slow folding reactions. Additionally, structural information on the folding events that occurred within the experimental dead time was indirectly accessed by comparative analysis of kinetic and steady-state refolding data. At slightly destabilizing refolding temperatures of 45 degrees C, which is close to the unfolding transition region, no specific secondary or tertiary structure is formed within 180 ms. After this delay all infrared markers bands diagnostic for individual structural elements indicate a strongly cooperative and relatively fast folding, which is not complicated by the accumulation of intermediates. At strongly native folding temperatures of 20 degrees C, a folding species of RNase T1 is detected within the dead time, which already possesses significant amounts of antiparallel beta-sheets, turn structures, and to some degree tertiary contacts. The early formed secondary structure is supposed to comprise the core region of the five-stranded beta-sheet. Despite these nativelike characteristics the subsequent refolding events are strongly heterogeneous and slow. The refolding under strongly native conditions is completed by an extremely slow formation or rearrangement of a locally restricted beta-sheet region accompanied by the further consolidation of turns and denser backbone packing. It is proposed that these late events comprise the final packing of strand 1 (residues 40-42) of the five-stranded beta-sheet against the rest of this beta-sheet system within an otherwise nativelike environment. This conclusion was supported by the comparison of refolding of RNase T1 and its variant W59Y RNase T1 that enabled the assignment of these very late events to the trans-->cis isomerization reaction of the prolyl peptide bond preceding Pro-39.

Calcium-dependent and -independent interactions of the calmodulin-binding domain of cyclic nucleotide phosphodiesterase with calmodulin

The ubiquitous Ca2+-binding regulatory protein calmodulin (CaM) binds and activates a wide range of regulatory enzymes. The binding is usually dependent on the binding of Ca2+ to CaM; however, some target proteins interact with CaM in a calcium-independent manner. In this work, we have studied the interactions between CaM and a 20-residue synthetic peptide encompassing the major calmodulin-binding domain of cyclic nucleotide phosphodiesterase (PDE1A2). The binding was studied in the absence and presence of Ca2+ by far-UV and near-UV circular dichroism, fluorescence, and infrared spectroscopy. In addition, two-dimensional heteronuclear NMR studies with 13C-methyl-Met-CaM and uniformly 15N-labeled CaM were performed. Competition assays with smooth muscle myosin light chain kinase revealed a Kd of 224 nM for peptide binding to Ca2+-CaM, while binding of the peptide to apo-CaM is weaker. The peptide binds with an alpha-helical structure to both lobes of Ca2+-saturated CaM, and the single Trp residue is firmly anchored into the C-terminal lobe of CaM. In contrast, the Trp residue plays a minor role in the binding to the apo-protein. Moreover, when bound to apo-CaM, the PDE peptide is only partially helical, and it interacts solely with the C-terminal lobe of CaM. These results show that the Ca2+-induced activation of PDE involves a significant change in the structure and positioning of the CaM-bound PDE peptide domain.

Two-dimensional mid-IR and near-IR correlation spectra of ribonuclease A: using overtones and combination modes to monitor changes in secondary structure

We introduce near-IR spectroscopy as an ancillary tool for monitoring structural changes of proteins in aqueous solution using ribonuclease A (RNase A) as a model protein. The thermal unfolding of RNase A results in clear spectral changes in the near-IR and the mid-IR regions. In the near-IR the most pronounced changes are observed in the spectral region between 4820 and 4940 cm-1. The strong N-H combination band found at 4867 cm-1 in the spectrum of native RNase A shifts to 4878 cm-1 upon thermal unfolding. Hydrogen-deuterium exchange experiments that validate the N-H character of this mode can also be used to estimate the number of unexchanged amide protons after exposure to D2O. The transition profiles and temperatures derived from the temperature dependence of the N-H combination mode were found to be practically identical with those derived from the temperature dependence of the C = O amide I band in the mid-IR region, demonstrating that the near-IR region can be used as a conformation-sensitive monitor for the thermally induced unfolding of proteins in H2O solution. A 2-dimensional correlation analysis was applied to the mid-IR and near-IR spectra of RNase A to establish correlations between IR bands in both regions. The correlation analysis demonstrates that the thermal unfolding of RNase A is not a completely cooperative process; rather it begins with some changes in beta-sheet structure, followed by the loss of alpha-helical structures, and then ending with the unfolding of the remaining beta-sheets.

Refolding of thermally and urea-denatured ribonuclease A monitored by time-resolved FTIR spectroscopy

We undertook a first detailed comparative analysis of the refolding kinetics of ribonuclease A (RNase A) by time-resolved Fourier transform infrared spectroscopy. The refolding process was initiated either by applying a temperature jump on the thermally denatured protein or by rapid dilution of a concentrated [13C]urea solution containing the chemically unfolded protein. The dead time of the injecting and mixing devices and the time-resolution of the spectrometer permitted us to monitor the refolding kinetics in a time range of 100 ms to minutes. The infrared amide I' band at 1631 cm-1 was used to directly probe the formation of beta-sheet structure during the refolding process. The aromatic ring stretching vibration of tyrosine at 1515 cm-1 was employed as a local monitor that detects changes in the tertiary structure along the folding pathway. The comparative analysis of the kinetics of the beta-sheet formation of chemically and thermally denatured ribonuclease A revealed similar folding rates and amplitudes when followed under identical refolding conditions. Therefore, our kinetic infrared studies provide evidence for a high structural similarity of urea-denatured and heat-denatured RNase A, corroborating the conclusions derived from the direct comparison of the infrared spectra of thermally and chemically denatured RNase A under equilibrium conditions [Fabian, H., & Mantsch, H.H. (1995) Biochemistry 34, 13651-13655]. In detail, the kinetic infrared data demonstrate that in the time window of 0.1-30 s approximately 40% of the native beta-sheet structure in RNase A is formed in the presence of 0.6 M urea at pH* 3.6, indicating that up to 60% of the beta-structure is formed out of the time window used in this study. Temperature jump experiments in the absence of chemical denaturants exhibited faster and more complex refolding kinetics. In addition, differences in the time constants of refolding derived from the amide I' band at 1631 cm-1 and from the tyrosine vibration at 1515 cm-1 were observed, indicating that the formation of secondary structure precedes the formation of stable tertiary contacts during the refolding of RNase A.

Conformation of a water-soluble beta-sheet model peptide. A circular dichroism and Fourier-transform infrared spectroscopic study of double D-amino acid replacements

Among peptide secondary structures beta-sheet domains have been much less intensively studied than alpha-helical conformations, mainly because of the lack of well characterized model peptides. In the present paper the secondary structure of a water-soluble de novo peptide consisting of 26 amino acids (DPKGDPKGVTVTVTVTVTGKGDPKPD-NH2) and the corresponding double D-amino acid replacement set have been studied by circular dichroism and Fourier-transform infrared spectroscopy. The model peptide was found to be unstructured in aqueous solution at peptide concentrations < 10(-3) mol/L but to adopt a predominantly beta-sheet structure in the presence of 15 mM sodium dodecyl sulfate or at apolar/water interfaces. Although the peptide is composed of amino acids with low helical propensity, it formed a single-stranded helical structure in aqueous trifluoroethanol. The D-amino acid replacement set was synthesized in order to study the conformational stability of the model peptide selectively in distinct regions. The data show that both the alpha-helix present in 50% trifluoroethanol as well as the beta-sheet domain formed in the presence of sodium dodecyl sulfate or at apolar/water interfaces, are located in the region between Val9 and Thr18. Pairwise substitution of adjacent amino acids by their corresponding D-amino acids provides a pronounced beta-sheet disturbance. These findings demonstrate that double D-amino acid replacements may be used to locate beta-sheet domains in peptides.

Protein structural segments and their interconnections derived from optical spectra. Thermal unfolding of ribonuclease T1 as an example

A novel descriptor for protein structure is examined here that goes beyond predictions of the average fractional components (FC) of a few conformational types and represents the number and interconnection of segments of continuous, well-defined secondary structural elements such as alpha-helices and beta-sheets. This matrix descriptor can be predicted from optical spectra using neural network methods. The new matrix plus traditional FC descriptors can be quickly and generally obtained to provide a level of detail not previously derived from optical spectra and a discrimination between proteins that might otherwise be viewed as being very similar using just the FC descriptor. As an example of its potential utilization, this matrix descriptor approach was applied to an analysis of both the native state and the reversible thermal denaturation of ribonuclease T1 in H2O. Analyses of the FTIR spectral data indicate initial loss of the major helical segment at 50-55 degrees C but with little accompanying change in the number of sheet segments or the sheet FC values. Circular dichroism (CD) and vibrational CD data are also used to support this interpretation based on FC changes with temperature. Parallel analysis of the corresponding data for this protein in D2O demonstrates that the method is sensitive to the match between the degree of H-D exchange used to prepare samples for the unknown and the reference data set.

Structural properties of UMP-kinase from Escherichia coli: modulation of protein solubility by pH and UTP

UMP-kinase from Escherichia coli, unlike the analogous enzyme from eukaryotic organisms, is an oligomeric protein subjected to complex regulatory mechanisms in which UTP and GTP act as allosteric effectors. While the enzyme has an unusually low solubility at neutral pH (< or = 0.1 mg of protein/ mL), its solubility increases markedly above pH 8 and below pH 4. Furthermore, the solubility of the bacterial UMP-kinase at neutral pH is greatly enhanced in the presence of Mg-free UTP. Thermal denaturation experiments have demonstrated that UTP also increases the stability of the protein. Fourier-transform infrared spectroscopy and circular dichroism show that the secondary structure of the protein is the same at neutral and at alkaline pH. These data indicate that variations in enzyme solubility must be related to subtle changes in the tertiary and/or quaternary structure which modulate the exposure of hydrophobic surfaces in the protein molecule. A variant of UMP-kinase, obtained by site-directed mutagenesis (Asp159Asn), which is similar to the wild-type enzyme in its stability and kinetic properties, has a much increased water solubility (> 5 mg protein/mL) even at neutral pH. This suggests that salt bridges may be involved in the equilibrium between the soluble and aggregated forms of the wild-type enzyme, and that conformational changes induced upon binding of UTP increase the protein solubility by disrupting these salt bridges.

Conformational differences of ovine and human corticotropin releasing hormone. A CD, IR, NMR and dynamic light scattering study

The differences in the conformational properties of ovine (o) and human (h) CRH in aqueous solution, structure-inducing TFE and in the presence of detergent micelles and lipid vesicles have been investigated by circular dichroism, Fourier transform infrared spectroscopy, NMR and dynamic light scattering. o-CRH was found to exist as a monomer with little regular structure in dilute aqueous solution. Association at concentrations higher than 10-3 mol/L results predominantly in dimers. The induction of a substantial amount of intermolecular beta-structure seems to be the result of interactions of the C-terminal hexapeptide and the N-terminal region 6-12 of o-CRH chains in antiparallel orientation. In contrast, h-CRH exhibits a high tendency of association which is highly sensitive to the pH. The formation of tetramers at millimolar peptide concentration is related to a helical content of ca. 50%. The potentially helical, highly hydrophobic region 6-20 enlarged by more hydrophobic residues in position 23 and 25 is proposed to stabilize the h-CRH associates. In the presence of structure inducing TFE (> 40% v) both CRH peptides exist as monomers. o-CRH reveals about 72% helicity, in h-CRH the formation of about 85% helix is observed. The differences in helicity of the two CRH molecules are located in the C-terminal heptapeptide, as concluded on the basis of NMR studies. Both peptides bind to detergent micelles at pH 4 as well as 7.4 associated with an increase in the alpha-helical content. Interaction of the two peptides with DMPC vesicles was found exclusively at pH 4. Above the phase transition temperature of DMPC the alpha-helical content in h-CRH increases slightly; however, o-CRH reveals a substantial amount of beta-type structure. The intramolecular type of beta-structure is associated with a deeper insertion of the o-CRH region 6-12 into the hydrophobic region of the lipid bilayer, whereas the corresponding region of h-CRH is kept in the bilayer surface. The higher helicity of h-CRH might explain to some extent its higher affinity to the CRH receptor, CRH antibodies and the CRH binding protein.

Comparative analysis of the amino- and carboxy-terminal domains of calmodulin by Fourier transform infrared spectroscopy

Fourier transform infrared spectra were obtained for mammalian calmodulin and two of its fragments produced by limited proteolysis with trypsin TR1C (1-77) and TR2C (78-148). Experiments were done in H2O, D2O and D2O/trifluoroethanol (TFE) mixtures. Information about secondary structure was obtained from analysis of the amide I and II bands; while characteristic absorbances for tyrosine, phenylalanine and carboxylate groups were analyzed for changes in tertiary structure. Our data indicate that the secondary and tertiary structure is preserved in the two half molecules of CaM, both in the apo- and Ca(2+)-saturated state. Addition of the structure-inducing solvent TFE causes marked changes only in the apo-TR1C domain. The maximum wavenumber for the amide I band of the two domains of CaM in D2O was markedly different (1642 cm-1 for TR1C versus 1646/1648 cm-1 for Ca2+ and apo-TR2C). This renders the amide I band for the intact protein very broad in comparison to that in other proteins and is indicative of a distribution of alpha-helices with slightly different hydrogen bonding patterns.

Thermally induced hydrogen exchange processes in small proteins as seen by FTIR spectroscopy

Fourier-transform infrared (FTIR) spectroscopy has been used to study the thermally induced exchange characteristics of those backbone amide protons which persist H-D exchange at ambient conditions in ribonuclease A, in wild type ribonuclease T1 and some of its variants, and in the histone-like protein HBsu. The H-D exchange processes were induced by increasing the thermal energy of the protein solutions in two ways: (i) by linearly increasing the temperature, and (ii) by a temperature jump. To trace the H-D exchange in the proteins, various infrared absorption bands known to be sensitive to H-D exchange were used as specific monitors. Characteristic H-D exchange curves were obtained from which the endpoints (TH/D) of H-D exchange could be determined. The H-D exchange curves, the TH/D-values and the phase transition temperatures Tm were used to estimate the structural flexibility and stability of the given proteins. It is suggested that time-resolved FTIR spectroscopy can be used to determine global stability parameters of proteins.

Ribonuclease A revisited: infrared spectroscopic evidence for lack of native-like secondary structures in the thermally denatured state

To address a number of conflicting reports in the literature, we undertook an infrared spectroscopic study to test for the presence of native-like secondary structures in thermally denatured ribonuclease A. Ribonuclease A does not aggregate at high temperatures, and the infrared spectrum shows a completely featureless amide I band contour. Using 13C-labeled urea, we were also able to obtain the infrared spectrum of the chemically denatured protein, which is practically identical with that of the heat-denatured protein. To the best of our knowledge, this is the first study that uses 13C-labeled urea as a chemical denaturant which circumvents the problem encountered with the strong absorption of urea in the conformation-sensitive amide I region of proteins; it opens up the possibility of investigating protein folding/unfolding processes in the presence of high concentrations of chemical denaturants. From an analysis of the amide I region of the infrared spectra of thermally and chemically denatured RNase A, it was concluded that heat-denatured ribonuclease A does not contain any significant amount of authentic hydrogen-bonded secondary structures. Furthermore, a comparison of the infrared spectra of ribonuclease A with those of ribonuclease T1 demonstrates that in spite of major differences between their native structures there are practically no differences between their heat-denatured states. This would not be expected if there were residual native-like secondary structures in the thermally denatured state of one or both of these proteins.

Temperature-jump-induced refolding of ribonuclease A: a time-resolved FTIR spectroscopic study

FTIR difference spectroscopy has been used for the first time to investigate the kinetics of secondary structure formation during refolding. The refolding process of ribonuclease A (RNase A) as a model system was induced by applying a temperature-jump of 60 degrees. The temperature-jump was triggered by rapidly injecting a small volume of the thermally unfolded protein solution at 80 degrees C into a special cuvette system kept at 20 degrees C. The dead-time of the injection and the time resolution of the FTIR spectrometer permitted the observation of refolding processes in a time window ranging from 170 ms to several minutes. Specifically, the formation of beta-structures and the disappearance of irregular conformations could be observed in this time interval.

Aspartate-bond isomerization affects the major conformations of synthetic peptides

The aspartic acid bond changes to an beta-aspartate bond frequently as a side-reaction during peptide synthesis and often as a post-translational modification of proteins. The formation of beta-asparate bonds is reported to play a major role not only in protein metabolism, activation and deactivation, but also in pathological processes such as deposition of the neuritic plaques of Alzheimer's disease. Recently, we reported how conformational changes following the aspartic-acid-bond isomerization may help the selective aggregation and retention of the amyloid beta peptide in affected brains (Fabian et al., 1994). In the current study we used circular dichroism, Fourier-transform infrared spectroscopy, and molecular modeling to characterize the general effect of the beta-aspartate-bond formation on the conformation of five sets of synthetic model peptides. Each of the non-modified, parent peptides has one of the major secondary structures as the dominant spectroscopically determined conformation: a type I beta turn, a type II beta turn, short segments of alpha or 3(10) helices, or extended beta strands. We found that both types of turn structures are stabilized by the aspartic acid-bond isomerization. The isomerization at a terminal position did not affect the helix propensity, but placing it in mid-chain broke both the helix and the beta-pleated sheet with the formation of reverse turns. The alteration of the geometry of the lowest energy reverse turn was also supported by molecular dynamics calculations. The tendency of the aspartic acid-bond isomerization to stabilize turns is very similar to the effect of incorporating sugars into synthetic peptides and suggests a common feature of these post-translational modifications in defining the secondary structure of protein fragments.

Tyrosine- versus serine-phosphorylation leads to conformational changes in a synthetic tau peptide

One of the major immunodominant epitopes of the paired helical filaments (PHF) of Alzheimer's disease is the peptide sequence GAEIVYKSPVVSGD (T3), comprising amino acids 389-402 of the microtubule-associated protein, tau, when it is phosphorylated at the first serine residue. While the corresponding anti-PHF monoclonal antibody recognizes the peptide phosphorylated at either serine, it does not recognize the tyrosine-phosphorylated peptide. Here we describe the effect of serine- versus tyrosine-phosphorylation on the conformation of a synthetic tau peptide. While adding a phosphate to the serine residue has practically no impact on the structure of the non-phosphorylated peptide, phosphorylation of the tyrosine results in considerable conformational changes.

Isotope-edited Fourier transform infrared spectroscopy studies of calmodulin's interaction with its target peptides

The ubiquitous calcium-binding protein calmodulin (CaM) regulates a wide variety of cellular events by binding to and activating many distinct target enzymes. The CaM-binding domains of most of these enzymes are contained in a contiguous stretch of amino acids with a length of approximately 20 residues. In this work, we have used "isotope-edited" Fourier transform infrared spectroscopy to study the interaction of CaM with synthetic peptides resembling the CaM-binding domains of myosin light chain kinase (MLCK), constitutive nitric oxide synthase (cNOS), and caldesmon (CaD). Uniform labeling of CaM with carbon-13 causes the amide I band of the protein to shift approximately 55 cm-1 to lower frequency in D2O, leaving a clear window in the infrared spectrum for observing the amide I band of the unlabeled target peptides. Upon complex formation, the amide I bands of the CaM-binding domains of MLCK and cNOS shift 4 cm-1 toward higher frequency (to approximately 1648 cm-1), and have a narrower bandwidth compared to the peptide in aqueous solution. These spectral changes and the fact that the infrared spectra of these two peptides in their complex with CaM closely resemble those recorded in a mixture of D2O and the helix inducing solvent trifluoroethanol indicate that they bind to CaM in an alpha-helical conformation. The CaM-binding domain of CaD also showed similar, but less dramatic, spectral changes; this is in agreement with the fact that it binds to CaM with lower affinity and a shorter alpha-helix.(ABSTRACT TRUNCATED AT 250 WORDS)

Impact of point mutations on the structure and thermal stability of ribonuclease T1 in aqueous solution probed by Fourier transform infrared spectroscopy

We undertook a detailed comparative analysis of the infrared spectra of wild-type ribonuclease T1 and three mutants: two single mutants, Tyr-45-->Trp (Y45W) and Trp-59-->Tyr (W59Y), and a double mutant, Tyr-45-->Trp/Trp-59-->Tyr (Y45W/W59Y). These mutants were selected because they are known to affect the activity of the enzyme. The structural differences were evaluated by using peptide backbone and side-chain "marker" bands as conformation-sensitive monitors. All mutations lead to a decrease of the thermal transition temperature, though the mutation Tyr-45-->Trp affects the Tm to a lesser degree than the replacement of Trp-59 by Tyr, both in the single (W59Y) and in the double (Y45W/W59Y) mutant. Small changes in the protein backbone conformation and in the microenvironment of certain amino acids, induced by the point mutations, could be detected. In particular, we found subtle differences in the hydrogen bonding pattern of the beta-strands in the mutants W59Y and Y45W/W59Y, compared to that in wild-type RNase T1 and in the mutant Y45W. Practically identical spectra in the amide I region were obtained for the double mutant Y45W/W59Y and the single mutant W59Y, demonstrating that it is the change from Trp to Tyr in position 59 (located at the interface between the alpha-helix and a beta-strand) which affects the overall protein conformation. The mutation Tyr to Trp in position 45, on the other hand, has practically no impact on the polypeptide backbone conformation.(ABSTRACT TRUNCATED AT 250 WORDS)

Zinc chelation and structural stability of adenylate kinase from Bacillus subtilis

Adenylate kinase from Bacillus subtilis, like the enzyme from Bacillus stearothermophilus, contains a structural zinc atom. Cys153 in the enzyme from B. stearothermophilus, which is involved in the zinc coordination, is replaced in the adenylate kinase from B. subtilis by an aspartic acid residue. Therefore, we were interested in establishing whether this difference has an impact on the structure, the metal chelation, and the overall stability of these proteins. We also were interested in determining whether His138, which is conserved in many adenylate kinases, can act as a fourth partner in the metal chelation and, in general, whether His can successfully replace Cys or Asp in coordinating zinc in the adenylate kinase from B. subtilis. The adk gene from B. subtilis was cloned by polymerase chain reaction. The wild-type protein, together with several variants obtained by site-directed mutagenesis, were expressed in Escherichia coli and analyzed by biochemical and physicochemical methods. The H138N and D153C mutants of adenylate kinase from B. subtilis exhibited properties similar to those of the wild-type protein, indicating that His138 is not involved in metal coordination and that Asp153, just like Cys in the analogous position in the enzyme from B. stearothermophilus, can participate in zinc chelation. This is the first experimental evidence indicating that aspartic acid can be involved in the coordination of a structural zinc atom. On the other hand, the D153H and D153T variants showed significant changes in their zinc-binding properties. Dialysis of the latter proteins against buffer (in both the presence and the absence of 2 mM EDTA) resulted in removal of the metal ion and loss of enzymatic activity.(ABSTRACT TRUNCATED AT 250 WORDS)

Synthetic post-translationally modified human A beta peptide exhibits a markedly increased tendency to form beta-pleated sheets in vitro

The beta-amyloid peptide (A beta) is the major constituent of senile plaques, one of the hallmark neuropathological lesions of Alzheimer's disease. Recently a post-translationally modified analogue of the human beta-amyloid peptide, which contains isoaspartic residues in positions 1 and 7, was isolated from parenchyma and leptomeningeal microvasculature of Alzheimer's disease patients [Roher, A. E., Lowenson, JD., Clarke, S., Wolkow, C., Wang, R., Cotter, R. J., Reardon, I. M., Zürcher-Neely, H. A., Heinrikson, R. L., Ball, M. J. & Greenberg, B. D. (1993) J. Biol. Chem. 268, 3072-3083]. We used circular dichroism and Fourier-transform infrared spectroscopy to characterize the conformational changes on human A beta upon substitution of Asp1 and Asp7 to isoaspartic residues. We found that the intermolecular beta-pleated-sheet content is markedly increased for the post-translationally modified peptide compared to that in the corresponding unmodified human or rodent A beta sequences both in aqueous solutions in the pH 7-12 range, and in membrane-mimicking solvents (such as aqueous octyl-beta-D-glucoside or aqueous acetonitrile solutions). These findings underline the importance of the originally alpha-helical N-terminal regions of the unmodified A beta peptides in defining its secondary structure and may offer an explanation for the selective aggregation and retention of the isomerized A beta peptide in Alzheimer's-disease-affected brains.

Structural and physico-chemical characteristics of Bordetella pertussis adenylate kinase, a tryptophan-containing enzyme

The adk gene from the Gram-negative pathogen Bordetella pertussis was cloned by complementing the thermosensitive Escherichia coli adk strain CR341T28. B. pertussis adenylate kinase is a 218-amino-acid protein that has high similarity with adenylate kinase from Escherichia coli and Hemophilus influenzae (57%). A distinct characteristic of enzyme from B. pertussis, not found in other bacterial adenylate kinases, is the presence of a tryptophan residue at position 185. Although distant from the catalytic site, this single tryptophan serves as a convenient probe for monitoring the binding of nucleotide substrates or analogs to the enzyme. Differential scanning calorimetry and equilibrium unfolding experiments in guanidine.HCl indicate similar stabilities for adenylate kinase from B. pertussis and E. coli. An extensive comparison between physico-chemical properties of adenylate kinase from B. pertussis and the enzyme from E. coli showed that the kinetic and structural properties of the two enzymes are very similar. However, infrared spectroscopy has allowed to identify small but significant differences in the secondary structure of the two proteins.

Secondary structure and temperature-induced unfolding and refolding of ribonuclease T1 in aqueous solution. A Fourier transform infrared spectroscopic study

The secondary structure of ribonuclease T1 (RNase T1) in aqueous solution and its temperature-induced structural changes have been investigated by Fourier-transform infrared (FT-IR) spectroscopy. 13 to 14% alpha-helix and 32 to 33% beta-sheet were estimated from the resolution-enhanced FT-IR spectra, in agreement with the crystal structure which indicates 16% alpha-helix and 35% beta-sheet. Specific IR-marker bands are assigned to the different beta-sheet structures, to the slightly bent alpha-helix, and to beta-turn and irregular conformations present in RNase T1. The temperature dependence of the infrared spectra shows that the thermal unfolding and refolding of RNase T1 is fully reversible. This permitted the detailed analysis of structural changes that occur as a function of temperature by evaluating quantitatively the various secondary structure-related amide I band components and some amino acid side-chain vibrations as specific monitors. The secondary structure of RNase T1 is essentially retained in the temperature range between 20 and 50 degrees C. Significant perturbation of protein structure is initiated between 50 and 55 degrees C within regions of beta-sheet structures while the alpha-helix remains virtually intact up to 55 degrees C suggesting a "premelting" of RNase T1. Between 55 and 60 degrees C, a highly co-operative unfolding process is indicated by the simultaneous breakdown of all secondary structure components and by distinct changes of some specific side-chain vibrations. An analysis of the amide I band contour of RNase T1 at 70 degrees C proves that the unfolded state is predominantly, but not completely, irregular or "random coil". Residual, turn-like structures persisting even in the unfolded state are suggested by minor, turn related band components in the amide I region. From IR-spectra collected along a linear temperature gradient, intensity/temperature and frequency/temperature profiles were constructed using some peptide backbone and amino acid side-chain marker bands as local, structure-sensitive monitors. From these profiles individual transition temperatures tm and transition enthalpies delta H (van't Hoff) were calculated. The tm and delta H values revealed a small but distinct hysteresis between repetitive cycles of unfolding and refolding of the protein, suggesting slow refolding kinetics of RNase T1. Furthermore, the various infrared "marker bands" indicate a slightly different response towards temperature increase/decrease for different regions of the protein. The data demonstrate that infrared spectroscopy permits both the detailed analysis of structural changes occurring in a protein as a function of temperature and the determination of thermodynamic parameters characterizing its folded/unfolded state transition.

Comparative analysis of human and Dutch-type Alzheimer beta-amyloid peptides by infrared spectroscopy and circular dichroism

The 42 amino acid beta A4 peptide is the major constituent of the senile plaques, one of the hallmark neuropathological lesions of Alzheimer's disease. While C-terminally truncated variants were shown to be present in normal body fluids, a single Glu-->Gln change in the 39 amino acid form of beta A4 results in accelerated fibril formation in the brains of patients with Dutch-type hereditary cerebral hemorrhage with amyloidosis. In this study we used Fourier-transform infrared and circular dichroism spectroscopies on synthetic peptides to demonstrate that this mutation results in altered secondary structure in membrane mimicking solvents, characterized by a considerably higher beta-structure content for the mutant peptide. Moreover, extreme high and low pH were less effective in eliminating the beta-conformation for the Dutch-variant than for the normal human sequence.

Conformation of d(GGGATCCC)2 in crystals and in solution studied by X-ray diffraction, Raman spectroscopy and molecular modelling

In the crystal, d(GGGATCCC)2 forms an A-DNA double helix as known from a single crystal X-ray diffraction study. Accordingly, in the Raman spectra of crystals the A-family marker bands at 664, 705, 807 and 1101 cm-1 and the spectral characteristics in the region 1200 to 1500 cm-1 clearly demonstrate the A-form as the dominant conformation. Bands at 691, 850, and 1080 cm-1, however, indicate that a minor fraction of the octamer molecules in the crystal is in an unusual, still not unequivocally identified conformation possibly belonging to the B-family. In solution, the octamer is in B-like conformation as shown by the presence of B-DNA Raman marker bands at 685, 837, 1094 and 1421 cm-1. Molecular modelling techniques lead to three structures with slightly different B-form geometries as the lowest energies models when a sigmoidal dielectric function with the bulk dielectric constant epsilon = 78 and the value q = -0.5e for the effective phosphate charges was used in the calculations. An A-form structure bearing a strong resemblance to the experimentally determined crystal structure becomes the lowest energy model structure when the electrostatic parameters are changed to epsilon = 30 and q = -0.25e, respectively.

Secondary structure of streptokinase in aqueous solution: a Fourier transform infrared spectroscopic study

The secondary structure of streptokinase (Sk) in aqueous solution was quantitatively examined by using Fourier transform infrared (FT-IR) spectroscopy. Resolution enhancement techniques, including Fourier deconvolution and derivative spectroscopy, were combined with band curve-fitting procedures to quantitate the spectral information from the amide I bands. Nine component bands were found under the broad, nearly featureless amide I bands which reflect the presence of various substructures. The relative areas of these component bands indicate an amount of beta-sheet between 30 and 37% and an alpha-helix content of only 12-13% in Sk. Further conformational substructures are assigned to turns (25-26%) and to "random" structures (15-16%). Additionally, the correlation of a pronounced component band near 1640 cm-1 (10-16% fractional area) with the possible presence of 3(10)-helices is discussed.

Limited proteolysis of streptokinase and properties of some fragments

Limited proteolysis of streptokinase (Sk) by trypsin and thermolysin was performed under various incubation conditions and analysed by polyacrylamide gel electrophoresis. Several fragments (Sk1, Tr27, Tr17, Th26, and Th16) were isolated and characterized further. The N-terminal sequences of Tr27, Tr17, Th26, Th16 and the C-terminal sequences of Tr27 and Th26 were determined by partial sequencing. The evidence available allows the positioning of these fragments within the Sk sequence. Fragment Sk1 is obtained by carefully standardized tryptic digestion of Sk and gel chromatography under non-denaturing conditions. Sk1 is formed by a large polypeptide Ser60-Lys293 and non-covalently bonded smaller polypeptides composed of amino acids from the N-terminal region Ile1-Lys59 of Sk. Fragment Tr27 consists of the large polypeptide Ser60-Lys293 of Sk1, and can be obtained from Sk1 by removal of the smaller N-terminal polypeptides under denaturing conditions. Fragment Th26 is composed of amino acids Phe63-His291. The N-termini of fragments Tr17 and Th16 start with Glu148 and Ile151. From their electrophoretically-determined sizes it can be concluded that they most probably have the same C-terminal amino acids, Lys293 and His291, as fragments Tr27 and Th26, respectively. Secondary structure elements of similar composition were found in all the fragments studied using circular dichroism (c.d.) and infrared (i.r.) measurements. Differential scanning calorimetric (d.s.c.) measurements were performed in order to correlate the sequence regions of Sk to energetic folding units of the protein. Fragments Sk1, Tr27, Th26, Tr17, and Th16 show one melting peak in the temperature range from 42.8 to 46.1 degrees C (thermal unfolding stage). For fragment Sk1, this melting peak can be separated by deconvolution into two transitions at T1 = 46.1 degree C and T2 = 47.3 degrees C with delta H1 = 450 kJ/mol and delta H2 = 219 kJ/mol, respectively. Fragments Tr17 and Th16 show one two-state transition at T = 42.8 degrees C with delta H = 326 kJ/mol.

Conformational properties of streptokinase--secondary structure and localization of aromatic amino acids

The conformational properties of streptokinase (Sk) have been assessed by several spectroscopic techniques. A solvent accessibility of about 70% of the 22 Tyr residues was found by u.v. perturbation spectroscopy. Fluorescence spectroscopy indicates also the surface localization of the single Trp 6 residue. Circular dichroism (c.d.), infrared (i.r.), and Raman spectra were analysed in order to estimate the contents of secondary structure elements of Sk. Values in the range of 14-23% alpha-helices, 38-46% beta-structures, 10-30% turns and 12-23% residual structures were found. The characteristics of the c.d. spectrum support the classification of Sk as an alpha + beta protein. Effects of temperature, pH, and denaturants were studied by c.d. spectroscopy, and on spin-labelled Sk, by e.p.r. spectroscopy. Structural effects were induced at temperatures above 40 degrees C, pH values below 3.0 and urea concentrations above 2 M. At temperatures above 70 degrees C, at pH 2.1, and at urea and Gu.HCl concentrations of 7 M and 5 M, respectively, no further structural changes are revealed in the spectra. At temperatures around 50 degrees C, at pH 3.0, and denaturant concentrations of about 1 M Gu.HCl and 1 M to 2 M urea, c.d. effects were observed in the near-u.v. region indicating an increase in the asymmetry for aromatic amino acids in comparison with the structure of Sk in low ionic strength buffers at neutral pH, 20 degrees C and in the absence of denaturants. These effects were most pronounced for the temperature dependence of the c.d. spectra. E.p.r. spectroscopy has shown that loosening of the protein surrounding of the spin label already begins at 1 M urea and that the mobility of the spin label points to a structural change in Sk at 46 degrees C.

Transient 210-nm absorption in fused silica induced by high-power UV laser irradiation

Synthetic fused silica, exposed to high-power KrF excimer laser irradiation, shows the well-known induced absorption at 210 nm owing to E' center generation. Time-resolved absorption spectroscopy reveals that this induced absorption is transient in nature. The generation rate of E' centers depends strongly on the irradiation history, the OH content, and previous high-temperature processes. In order to explain the experimental observations, a nonabsorbing state of theE' center is postulated. The recovery of the induced optical absorption in high-OH fused silica is explained as a conversion from E' centers to these nonabsorbing centers.

Conserved unpaired adenine residues are important for ordered structures of 5S ribosomal RNA. An infrared study of the secondary and tertiary structure of Thermus thermophilus 5S rRNA

An improved set of infrared calibration spectra for the determination of G X C and A X U base pairs leads to 32 +/- 3 G X C (+ G X U) and 4 +/- 1 A X U base pairs for Thermus thermophilus 5S RNA in the presence and absence of Mg2+. These results give further support for the consensus secondary structure of 5S RNA recently proposed by several groups. T. thermophilus 5S RNA shows, in the presence of Mg2+, a distinct two-step thermal melting of its ordered structure. Based on new data about the stacking dependence of infrared intensities of unpaired ribonucleotides the spectral changes of the low-temperature transition should be explained by melting of stacked arrangements of unpaired bases and/or non-standard base pairs. Striking is the reduction in A stacking, which is not related to the melting of A X U base pairs, indicating the importance of the mostly conserved unpaired adenines for the Mg2+ stabilized higher-order structures especially within internal loops of 5S RNA.