Promoting Complex Problem Solving by Introducing Schema-Governed Categories of Key Causal Models.

The ability to recognize key causal models across situations is associated with expertise. The acquisition of schema-governed category knowledge of key causal models may underlie this ability. In an experimental study (n = 183), we investigated the effects of promoting the construction of schema-governed categories and how an enhanced ability to recognize the key causal models relates to performance in complex problem-solving tasks that are based on the key causal models. In a 2 × 2 design, we tested the effects of an adapted version of an intervention designed to build abstract mental representations of the key causal models and a tutorial designed to convey conceptual understanding of the key causal models and procedural knowledge. Participants who were enabled to recognize the underlying key causal models across situations as a result of the intervention and the tutorial (i.e., causal sorters) outperformed non-causal sorters in the subsequent complex problem-solving task. Causal sorters outperformed the control group, except for the subtask knowledge application in the experimental group that did not receive the tutorial and, hence, did not have the opportunity to elaborate their conceptual understanding of the key causal models. The findings highlight that being able to categorize novel situations according to their underlying key causal model alone is insufficient for enhancing the transfer of the according concept. Instead, for successful application, conceptual and procedural knowledge also seem to be necessary. By using a complex problem-solving task as the dependent variable for transfer, we extended the scope of the results to dynamic tasks that reflect some of the typical challenges of the 21st century.

Local and Large-Scale Conformational Dynamics in Unfolded Proteins and IDPs. II. Effect of Temperature and Internal Friction.

Internal dynamics of proteins are essential for protein folding and function. Dynamics in unfolded proteins are of particular interest since they are the basis for many cellular processes like folding, misfolding, aggregation, and amyloid formation and also determine the properties of intrinsically disordered proteins (IDPs). It is still an open question of what governs motions in unfolded proteins and whether they encounter major energy barriers. Here we use triplet-triplet energy transfer (TTET) in unfolded homopolypeptide chains and IDPs to characterize the barriers for local and long-range loop formation. The results show that the formation of short loops encounters major energy barriers with activation energies (Ea) up to 18 kJ/mol (corrected for effects of temperature on water viscosity) with very little dependence on amino acid sequence. For poly(Gly-Ser) and polySer chains the barrier decreases with increasing loop size and reaches a limiting value of 4.6 ± 0.4 kJ/mol for long and flexible chains. This observation is in accordance with the concept of internal friction encountered by chain motions due to steric effects, which is high for local motions and decreases with increasing loop size. Comparison with the results from the viscosity dependence of loop formation shows a negative correlation between Ea and the sensitivity of the reaction to solvent viscosity (α) in accordance with the Grote-Hynes theory of memory friction. The Arrhenius pre-exponential factor (A) also decreases with increasing loop size, indicating increased entropic costs for loop formation. Long-range loop formation in the investigated sequences derived from IDPs shows increased Ea and A compared with poly(Gly-Ser) and polySer chains. This increase is exclusively due to steric effects that cause additional internal friction, whereas intramolecular hydrogen bonds, dispersion forces, and charge interactions do not affect the activation parameters.

Local and Large-Scale Conformational Dynamics in Unfolded Proteins and IDPs. I. Effect of Solvent Viscosity and Macromolecular Crowding.

Protein/solvent interactions largely influence protein dynamics, particularly motions in unfolded and intrinsically disordered proteins (IDPs). Here, we apply triplet-triplet energy transfer (TTET) to investigate the coupling of internal protein motions to solvent motions by determining the effect of solvent viscosity (η) and macromolecular crowding on the rate constants of loop formation (kc) in several unfolded polypeptide chains including IDPs. The results show that the viscosity dependence of loop formation depends on amino acid sequence, loop length, and co-solute size. Below a critical size (rc), co-solutes exert a maximum effect, indicating that under these conditions microviscosity experienced by chain motions matches macroviscosity of the solvent. rc depends on chain stiffness and reflects the length scale of the chain motions, i.e., it is related to the persistence length. Above rc, the effect of solvent viscosity decreases with increasing co-solute size. For co-solutes typically used to mimic cellular environments, a scaling of kc ∝ η-0.1 is observed, suggesting that dynamics in unfolded proteins are only marginally modulated in cells. The effect of solvent viscosity on kc in the small co-solute limit (below rc) increases with increasing chain length and chain flexibility. Formation of long and very flexible loops exhibits a kc ∝ η-1 viscosity dependence, indicating full solvent coupling. Shorter and less flexible loops show weaker solvent coupling with values as low as kc ∝ η-0.75 ± 0.02. Coupling of formation of short loops to solvent motions is very little affected by amino acid sequence, but solvent coupling of long-range loop formation is decreased by side chain sterics.

A Log File Analysis on the Validity of Partial Solutions in Figural Matrices Tests.

As a component of many intelligence test batteries, figural matrices tests are an effective way to assess reasoning, which is considered a core ability of intelligence. Traditionally, the sum of correct items is used as a performance indicator (total solution procedure). However, recent advances in the development of computer-based figural matrices tests allow additional indicators to be considered for scoring. In two studies, we focused on the added value of a partial solution procedure employing log file analyses from a computer-based figural matrices test. In the first study (n = 198), we explored the internal validity of this procedure by applying both an exploratory bottom-up approach (using sequence analyses) and a complementary top-down approach (using rule jumps, an indicator taken from relevant studies). Both approaches confirmed that higher scores in the partial solution procedure were associated with higher structuredness in participants' response behavior. In the second study (n = 169), we examined the external validity by correlating the partial solution procedure in addition to the total solution procedure with a Grade Point Average (GPA) criterion. The partial solution procedure showed an advantage over the total solution procedure in predicting GPA, especially at lower ability levels. The implications of the results and their applicability to other tests are discussed.

Delayed development of basic numerical skills in children with developmental dyscalculia.

Research suggests that children with developmental dyscalculia (DD) have deficits in basic numerical skills. However, there is conflicting evidence on whether basic numerical skills in children with DD are qualitatively different from those in typically developing children (TD) or whether basic numerical skills development in children with DD is simply delayed. In addition, there are also competing hypotheses about deficits in basic numerical skills, assuming (1) a general deficit in representing numerosities (Approximate Number System, ANS), (2) specific deficits in an object-based attentional system (Object Tracking System, OTS), or (3) deficits in accessing numerosities from symbols (Access Deficit, AD). Hence, the purpose of this study was to investigate whether deficits in basic numerical skills in children with DD are more indicative of a developmental delay or a dyscalculia-specific qualitative deviation and whether these deficits result from (selective) impairment of core cognitive systems involved in numerical processing. To address this, we tested 480 children (68 DD and 412 TD) in the 2nd, 3rd, and 4th grades with different paradigms for basic numerical skills (subitizing, counting, magnitude comparison tasks, number sets, and number line estimation tasks). The results revealed that DD children's impairments did not indicate qualitatively different basic numerical skills but instead pointed to a specific developmental delay, with the exception of dot enumeration. This result was corroborated when comparing mathematical profiles of DD children in 4th grade and TD children in 2nd grade, suggesting that DD children were developmentally delayed and not qualitatively different. In addition, specific deficits in core markers of numeracy in children with DD supported the ANS deficit rather than the AD and OTS deficit hypothesis.

The Fight against Infectious Diseases: The Essential Role of Higher-Order Thinking and Problem-Solving.

The development of a vaccine marks a breakthrough in the fight against infectious diseases. However, to eradicate highly infectious diseases globally, the immunization of large parts of the population is needed. Otherwise, diseases, such as polio, measles, or more recently COVID-19, will repeatedly flare-up, with devastating effects on individuals and, in the worst case, on significant shares of the world population. For example, polio has been almost eradicated over the past three decades through an unprecedented global effort, but complete immunization has not yet been achieved. In this article, we use polio as an example to show how the global effort of developing and administering a vaccine can be understood as solving a complex problem since it involves cultural, political, and geographical barriers that demand solutions in dynamically changing and highly versatile environments. Referring to the literature on problem-solving, higher-order thinking, and complex reasoning, we demonstrate how the ability to deal with real-world environments that are complex and dynamically changing, adapting initial solutions to new circumstances and collaborate efficiently with others, has been essential for this endeavor. We argue that problem-solving abilities form one basis for solving consequential world problems.

Thinking in action: Need for Cognition predicts Self-Control together with Action Orientation.

Need for Cognition describes relatively stable interindividual differences in cognitive motivation. Previous research has shown relations of Need for Cognition to Self-Control-a capacity that can be broadly defined as resistance to temptation-yet, the processes underlying this relation remain unclear. One explanation for the prediction of Self-Control by Need for Cognition can be an increased motivation to invest cognitive effort with higher levels of Need for Cognition. Another possible link could be that individual differences in the implementation of Self-Control intentions may play a moderating or mediating role for the predictive value of Need for Cognition. Such individual differences in the self-motivated initiation and maintenance of intentions are described by dispositional Action Orientation. Therefore, in the present study, Action Orientation was examined with regard to its possible role in explaining the relation of Need for Cognition to Self-Control. In a sample of 1209 young adults, Self-Control was assessed with two different self-report instruments and moderation and mediation models of the relationship between Need for Cognition, Action Orientation, and Self-Control were tested. While there was no evidence for a moderating role of Action Orientation in explaining the relation of Need for Cognition and Self-Control, Action Orientation was found to partly mediate this relation with a remaining direct effect of Need for Cognition on Self-Control. These results add to the conceptual understanding of Need for Cognition and demonstrate the relevance of trait variables to predict Self-Control.

A label-free LC/MS/MS-based enzymatic activity assay for the detection of genuine caspase inhibitors and SAR development.

The resurgence of interest in caspases (Csp) as therapeutic targets for the treatment of neurodegenerative diseases prompted us to examine the suitability of published nonpeptidic Csp-3 and Csp-6 inhibitors for our medicinal chemistry programs. To support this effort, fluorescence-based Csp-2, Csp-3, and Csp-6 enzymatic assays were optimized for robustness against apparent enzyme inhibition caused by redox-cycling or aggregating compounds. The data obtained under these improved conditions challenge the validity of previously published data on Csp-3 and Csp-6 inhibitors for all but one series, namely, the isatins. Furthermore, in this series, it was observed that the nature of the rhodamine-labeled substrate, typically used to measure caspase activity, interfered with the pharmacological sensitivity of the Csp-2 assay. As a result, a liquid chromatography/tandem mass spectrometry-based assay that eliminates label-dependent assay interference was developed for Csp-2 and Csp-3. In these label-free assays, the activity values of the Csp-2 and Csp-3 reference inhibitors were in agreement with those obtained with the fluorogenic substrates. However, isatin 10a was 50-fold less potent in the label-free Csp-2 assay compared with the rhodamine-based fluorescence format, thus proving the need for an orthogonal readout to validate inhibitors in this class of targets highly susceptible to artifactual inhibition.

Exploiting differences in caspase-2 and -3 S2 subsites for selectivity: structure-based design, solid-phase synthesis and in vitro activity of novel substrate-based caspase-2 inhibitors.

Several caspases have been implicated in the pathogenesis of Huntington's disease (HD); however, existing caspase inhibitors lack the selectivity required to investigate the specific involvement of individual caspases in the neuronal cell death associated with HD. In order to explore the potential role played by caspase-2, the potent but non-selective canonical Ac-VDVAD-CHO caspase-2 inhibitor 1 was rationally modified at the P(2) residue in an attempt to decrease its activity against caspase-3. With the aid of structural information on the caspase-2, and -3 active sites and molecular modeling, a 3-(S)-substituted-l-proline along with four additional scaffold variants were selected as P(2) elements for their predicted ability to clash sterically with a residue of the caspase-3 S(2) pocket. These elements were then incorporated by solid-phase synthesis into pentapeptide aldehydes 33a-v. Proline-based compound 33h bearing a bulky 3-(S)-substituent displayed advantageous characteristics in biochemical and cellular assays with 20- to 60-fold increased selectivity for caspase-2 and ∼200-fold decreased caspase-3 potency compared to the reference inhibitor 1. Further optimization of this prototype compound may lead to the discovery of valuable pharmacological tools for the study of caspase-2 mediated cell death, particularly as it relates to HD.

Fluorescent agonists for the Torpedo nicotinic acetylcholine receptor.

We have synthesized a series of fluorescent acylcholine derivatives carrying different linkers that vary in length and structure and connect the acylcholine unit to the environment-sensitive fluorophores 7-(diethylamino)coumarin-3-carbonyl (DEAC) or N-(7-nitrobenz-2-oxa-1,3-diazol-yl) (NBD). The pharmacological properties of the fluorescent analogues were investigated on heterologously expressed nicotinic acetylcholine receptor (nAChR) from Torpedo californica and on oocytes transplanted with nAChR-rich Torpedo marmorata membranes. Agonist action strongly depends on the length and the structure of the linker. One particular analogue, DEAC-Gly-C6-choline, showed partial agonist behavior with about half of the maximum response of acetylcholine, which is at least 20 times higher than those observed with previously described fluorescent dansyl- and NBD-acylcholine analogues. Binding of DEAC-Gly-C6-choline to Torpedo nAChR induces a strong enhancement of fluorescence intensity. Association and displacement kinetic experiments revealed dissociation constants of 0.5 nM for the alphadelta-binding site and 15.0 nM for the alphagamma-binding site. Both the pharmacological and the spectroscopic properties of this agonist show great promise for characterizing the allosteric mechanism behind the function of the Torpedo nAChR, as well as for drug-screening studies.

Using triplet-triplet energy transfer to measure conformational dynamics in polypeptide chains.

Intrachain diffusion processes play an important role in protein folding and function. In this chapter we discuss the application of triplet-triplet energy transfer to directly measure rate constants for intrachain contact formation in polypeptide chains. The photochemistry of triplet-triplet energy transfer is described, experimental prerequisites of the method are discussed, and a detailed description of the experimental protocols and data analysis is given.

Effect of proline and glycine residues on dynamics and barriers of loop formation in polypeptide chains.

Glycine and proline residues are frequently found in turn and loop structures of proteins and are believed to play an important role during chain compaction early in folding. We investigated their effect on the dynamics of intrachain loop formation in various unstructured polypeptide chains. Loop formation is significantly slower around trans prolyl peptide bonds and faster around glycine residues compared to any other amino acid. However, short loops are formed fastest around cis prolyl bonds with a time constant of 6 ns for end-to-end contact formation in a four-residue loop. Formation of short loops encounters activation energies in the range of 15 to 30 kJ/mol. The altered dynamics around glycine and trans prolyl bonds can be mainly ascribed to their effects on the activation energy. The fast dynamics around cis prolyl bonds, in contrast, originate in a higher Arrhenius pre-exponential factor, which compensates for an increased activation energy for loop formation compared to trans isomers. All-atom simulations of proline-containing peptides indicate that the conformational space for cis prolyl isomers is largely restricted compared to trans isomers. This leads to decreased average end-to-end distances and to a smaller loss in conformational entropy upon loop formation in cis isomers. The results further show that glycine and proline residues only influence formation of short loops containing between 2 and 10 residues, which is the typical loop size in native proteins. Formation of larger loops is not affected by the presence of a single glycine or proline residue.

Molecular basis for the effect of urea and guanidinium chloride on the dynamics of unfolded polypeptide chains.

Chemical denaturants are frequently used to unfold proteins and to characterize mechanisms and transition states of protein folding reactions. The molecular basis of the effect of urea and guanidinium chloride (GdmCl) on polypeptide chains is still not well understood. Models for denaturant--protein interaction include both direct binding and indirect changes in solvent properties. Here we report studies on the effect of urea and GdmCl on the rate constants (k(c)) of end-to-end diffusion in unstructured poly(glycine-serine) chains of different length. Urea and GdmCl both lead to a linear decrease of lnk(c) with denaturant concentration, as observed for the rate constants for protein folding. This suggests that the effect of denaturants on chain dynamics significantly contributes to the denaturant-dependence of folding rate constants for small proteins. We show that this linear dependency is the result of two additive non-linear effects, namely increased solvent viscosity and denaturant binding. The contribution from denaturant binding can be quantitatively described by Schellman's weak binding model with binding constants (K) of 0.62(+/-0.01)M(-1) for GdmCl and 0.26(+/-0.01)M(-1) for urea. In our model peptides the number of binding sites and the effect of a bound denaturant molecule on chain dynamics is identical for urea and GdmCl. The results further identify the polypeptide backbone as the major denaturant binding site and give an upper limit of a few nanoseconds for residence times of denaturant molecules on the polypeptide chain.

Dynamics of unfolded polypeptide chains as model for the earliest steps in protein folding.

The rate of formation of intramolecular interactions in unfolded proteins determines how fast conformational space can be explored during folding. Characterization of the dynamics of unfolded proteins is therefore essential for the understanding of the earliest steps in protein folding. We used triplet-triplet energy transfer to measure formation of intrachain contacts in different unfolded polypeptide chains. The time constants (1/k) for contact formation over short distances are almost independent of chain length, with a maximum value of about 5 ns for flexible glycine-rich chains and of 12 ns for stiffer chains. The rates of contact formation over longer distances decrease with increasing chain length, indicating different rate-limiting steps for motions over short and long chain segments. The effect of the amino acid sequence on local chain dynamics was probed by using a series of host-guest peptides. Formation of local contacts is only sixfold slower around the stiffest amino acid (proline) compared to the most flexible amino acid (glycine). Good solvents for polypeptide chains like EtOH, GdmCl and urea were found to slow intrachain diffusion and to decrease chain stiffness. These data allow us to determine the time constants for formation of the earliest intrachain contacts during protein folding.

Pyruvate decarboxylase from Kluyveromyces lactis. An enzyme with an extraordinary substrate activation behaviour.

Pyruvate decarboxylase (EC 4.1.1.1) was isolated and purified from the yeast Kluyveromyces lactis. The properties of this enzyme relating to the native oligomeric state, the subunit size, the nucleotide sequence of the coding gene(s), the catalytic activity, and protein fluorescence as well as circular dichroism are very similar to those of the well characterized pyruvate decarboxylase species from yeast. Remarkable differences were found in the substrate activation behaviour of the two pyruvate decarboxylases using three independent methods: steady-state kinetics, stopped-flow measurements, and kinetic dilution experiments. The dependence of the observed activation rate constant on the substrate concentration of pyruvate decarboxylase from K. lactis showed a minimum at a pyruvate concentration of 1.5 mm. According to the mechanism of substrate activation suggested this local minimum occurs due to the big ratio of the dissociation constants for the binding of the first (regulatory) and the second (catalytic) substrate molecule. The microscopic rate constants of the substrate activation could be determined by a refined fit procedure. The influence of the artificial activator pyruvamide on the activation of the enzyme was studied.