DRoP: a water analysis program identifies Ras-GTP-specific pathway of communication between membrane-interacting regions and the active site

Ras GTPase mediates several cellular signal transduction pathways and is found mutated in a large number of cancers. It is active in the GTP-bound state, where it interacts with effector proteins, and at rest in the GDP-bound state. The catalytic domain is tethered to the membrane, with which it interacts in a nucleotide-dependent manner. Here we present the program Detection of Related Solvent Positions (DRoP) for crystallographic water analysis on protein surfaces and use it to study Ras. DRoP reads and superimposes multiple Protein Data Bank coordinates, transfers symmetry-related water molecules to the position closest to the protein surface, and ranks the waters according to how well conserved and tightly clustered they are in the set of structures. Coloring according to this rank allows visualization of the results. The effector-binding region of Ras is hydrated with highly conserved water molecules at the interface between the P-loop, switch I, and switch II, as well as at the Raf-RBD binding pocket. Furthermore, we discovered a new conserved water-mediated H-bonding network present in Ras-GTP, but not in Ras-GDP, that links the nucleotide sensor residues R161 and R164 on helix 5 to the active site. The double mutant RasN85A/N86A, where the final link between helix 5 and the nucleotide is not possible, is a severely impaired enzyme, while the single mutant RasN86A, with partial connection to the active site, has a wild-type hydrolysis rate. DRoP was instrumental in determining the water-mediated connectivity networks that link two lobes of the catalytic domain in Ras.

Lengthening the intersubunit linker of procaspase 3 leads to constitutive activation

The conformational ensemble of procaspase 3, the primary executioner in apoptosis, contains two major forms, inactive and active, with the inactive state favored in the native ensemble. A region of the protein known as the intersubunit linker (IL) is cleaved during maturation, resulting in movement of the IL out of the dimer interface and subsequent active site formation (activation-by-cleavage mechanism). We examined two models for the role of the IL in maintaining the inactive conformer, an IL-extension model versus a hydrophobic cluster model, and we show that increasing the length of the IL by introducing 3-5 alanines results in constitutively active procaspases. Active site labeling and subsequent analyses by mass spectrometry show that the full-length zymogen is enzymatically active. We also show that minor populations of alternately cleaved procaspase result from processing at D169 when the normal cleavage site, D175, is unavailable. Importantly, the alternately cleaved proteins have little to no activity, but increased flexibility of the linker increases the exposure of D169. The data show that releasing the strain of the short IL, in and of itself, is not sufficient to populate the active conformer of the native ensemble. The IL must also allow for interactions that stabilize the active site, possibly from a combination of optimal length, flexibility in the IL, and specific contacts between the IL and interface. The results provide further evidence that substantial energy is required to shift the protein to the active conformer. As a result, the activation-by-cleavage mechanism dominates in the cell.

Thermodynamic, enzymatic and structural effects of removing a salt bridge at the base of loop 4 in (pro)caspase-3

Interactions between loops 2, 2' and 4, known as the loop bundle, stabilize the active site of caspase-3. Loop 4 (L4) is of particular interest due to its location between the active site and the dimer interface. We have disrupted a salt bridge between K242 and E246 at the base of L4 to determine its role in overall conformational stability and in maintaining the active site environment. Stability measurements show that only the K242A single mutant decreases stability of the dimer, whereas both single mutants and the double mutant demonstrate much lower activity compared to wild-type caspase-3. Structural studies of the caspase-3 variants show the involvement of K242 in hydrophobic interactions that stabilize helix 5, near the dimer interface, and the role of E246 appears to be to neutralize the positive charge of K242 within the hydrophobic cluster. Overall, the results suggest E246 and K242 are important in procaspase-3 for their interaction with neighboring residues, not with one another. Conversely, formation of the K242-E246 salt bridge in caspase-3 is needed for an accurate, stable conformation of loop L4 and proper active site formation in the mature enzyme.

Multiple solvent crystal structures of ribonuclease A: an assessment of the method

The multiple solvent crystal structures (MSCS) method uses organic solvents to map the surfaces of proteins. It identifies binding sites and allows for a more thorough examination of protein plasticity and hydration than could be achieved by a single structure. The crystal structures of bovine pancreatic ribonuclease A (RNAse A) soaked in the following organic solvents are presented: 50% dioxane, 50% dimethylformamide, 70% dimethylsulfoxide, 70% 1,6-hexanediol, 70% isopropanol, 50% R,S,R-bisfuran alcohol, 70% t-butanol, 50% trifluoroethanol, or 1.0M trimethylamine-N-oxide. This set of structures is compared with four sets of crystal structures of RNAse A from the protein data bank (PDB) and with the solution NMR structure to assess the validity of previously untested assumptions associated with MSCS analysis. Plasticity from MSCS is the same as from PDB structures obtained in the same crystal form and deviates only at crystal contacts when compared to structures from a diverse set of crystal environments. Furthermore, there is a good correlation between plasticity as observed by MSCS and the dynamic regions seen by NMR. Conserved water binding sites are identified by MSCS to be those that are conserved in the sets of structures taken from the PDB. Comparison of the MSCS structures with inhibitor-bound crystal structures of RNAse A reveals that the organic solvent molecules identify key interactions made by inhibitor molecules, highlighting ligand binding hot-spots in the active site. The present work firmly establishes the relevance of information obtained by MSCS.

Role of loop bundle hydrogen bonds in the maturation and activity of (Pro)caspase-3

During maturation, procaspase-3 is cleaved at D175, which resides in a linker that connects the large and small subunits. The intersubunit linker also connects two active site loops that rearrange following cleavage and, in part, form the so-called loop bundle. As a result of chain cleavage, new hydrogen bonds and van der Waals contacts form among three active site loops. The new interactions are predicted to stabilize the active site. One unresolved issue is the extent to which the loop bundle residues also stabilize the procaspase active site. We examined the effects of replacing four loop bundle residues (E167, D169, E173, and Y203) on the biochemical and structural properties of the (pro)caspase. We show that replacing the residues affects the activity of the procaspase as well as the mature caspase, with D169A and E167A replacements having the largest effects. Replacement of D169 prevents caspase-3 autoactivation, and its cleavage at D175 no longer leads to an active enzyme. In addition, the E173A mutation, when coupled to a second mutation in the procaspase, D175A, may alter the substrate specificity of the procaspase. The mutations affected the active site environment as assessed by changes in fluorescence emission, accessibility to quencher, and cleavage by either trypsin or V8 proteases. High-resolution X-ray crystallographic structures of E167A, D173A, and Y203F caspases show that changes in the active site environment may be due to the increased flexibility of several residues in the N-terminus of the small subunit. Overall, the results show that these residues are important for stabilizing the procaspase active site as well as that of the mature caspase.

The Swordsman at the Keyboard

The ability of music to install us in a continuous present is explored. Following Zuckerkandl, the musical whole is conceived as a field of forces, defined by the tensive relations among its constituent tones. Whether performing or only listening, in the true music experience our locus is always between tones, in the passage from one dynamic quality or state of incompleteness to the next. The moment-duration opens to cycle in tandem with the tonal design it embraces, tracking it from dynamic value to dynamic value, tracking “now.” Since waking time-outs from ordinary time may have a holistic healing function, music, as the most powerful medium of these events, may, after all, have survival value.

Contributions to the history of psychology: XLVII. Ignatius Loyola and behavior therapy

An early instance of what we call behavior therapy, devised by Ignatius Loyola, is noted.

Violence and prospect-refuge values

Appleton's prospect-refuge theory of landscape aesthetics is joined to Kupfer's treatment of the more contemporary forms of violence as aesthetic projects. The insufficiency in the modern urban environment of good opportunities to see without being seen stresses the present and near future into heightened feelings of vulnerability, adding with untoward social circumstance to activate more extreme measures to secure an advantage in our dealings with the world. From the standpoint of prospect-refuge theory, violence directed to asserting the self as someone who matters is a misbegotten effort to unstress the present and near future. Violence valued only for the aesthetic satisfaction in dismembering persons and things to formlessness suggests an attempt to kill time. As the likelihood of violent incidents increases, revisions in the prospect-refuge map together with institutional reforms become more urgent.

Contributions to Psychohistory: XII. the View from Betwixt and Between: J. M. Barrie and Humankind

In the world of betwixt and between nothing is ever so firmly fixed that it may not desert its proper post in space and time. From the far side of manhood, where the way opens into boyhood again, Barrie evolved ideas of considerable psychological value. General constructions, such as the lost middle act of life, the surrogate self, and the unlikely second chance, counsel courage to control the innate enemy, human frailty. Courage is “the lovely virtue.” The entrancing life has self-mastery for its goal. “Go out and fight,” he argues.

Sea Space and Transcendent Encounter

Sea space substitutes an optical equivalent of auditory perception for the normal visual experience. As tones do, the moving sea homogenizes space and creates values within the temporal horizon. The effect promotes the appearance of optical rhythm as a transcendent property which, coupled with the matching acoustical rhythm of the breaking waves, installs the observer in a continuous or prolonged present. A lifetime in this mode would convey the world permanently forming. Mythical statements of extraordinary transformations can be read as aesthetic responses to the lability of stimulus patterns at a time in a people's history when the transcendent mode is dominant, or at least most active. The sea is eminently labile and suggests infinite possibility. It cannot be dated and hints to us of eternity in our transcendent engagements with it.

Effect of Face-Masking on Aesthetic Judgment

Masked and unmasked university students, 11 women and 9 men in each group, applied a 20-scale form of the semantic differential to each of 10 paintings. Subjects chose their masks from eight articulated faces. On balance the pattern of differences in mean scale values for the two groups suggests that masking enhanced aesthetic awareness. Masked subjects judged the paintings significantly softer, more complex, more luminous, and sweeter. In a supplementary study 60 students, 40 women and 20 men, applied the same set of scales to the masks themselves. Alpha factoring, based on the mean ratings for all subjects, and equamax rotation was performed for scales as variables. Four factors emerged, in order: Temperament, Visual Tension, Evaluation and Dynamism. The mask most often chosen in Exp. I was judged most benign and most meaningful. Such a mask seems especially helpful to the aesthetic response.

Marcel Proust and Transcendent Encounter

Proust's moment bienheureux is a special case of transcendent being-in-the-world. The permanent essence of things supplies the transcendent properties. In the moment bienheureux time retains its place and person and world do not merge. Awareness is presentic, like movement in the prototypical transcendent act, the dance. Through the medium of the true self the personality returns to wholeness. Music furnishes the closest equivalent to the suggestions of personal truth that in the moment bienheureux betoken the possibility of living authentically.

Marcel Proust and the Problem of Time and Self

Proust conceived the true or permanent self to be a sensitiveness to the essence of things. Across this substratum moves a succession of temporary selves responsive to the accidental and evanescent. Continuity of being is traced to the memory. The true self is activated involuntarily and participates in experiences outside time. We eliminate the dimension of time when in remembering we introduce the past unchanged into the present. It is in the resonance of a former sensation, freshly occurring by chance, and the memorial representation of its prior existence, that we realize the most profound of life's truths. Through examining the past we can better know the true self and so redirect our temporal being.

Aesthetic Appreciation among Canadians and French: A Comparative Semantic Analysis

Canadian and French university students, 26 men and 94 women in each group, rendered aesthetic judgments of 20 Canadian and 20 French paintings. The instrument used was a 20-scale form of the semantic differential. Alpha factoring, based on the mean ratings, and varimax rotation was performed for scales as variables. For the Canadians four factors emerged in the order: Dynamism, Visual Tension, Tactility and Evaluation; for the French there were five: Visual Tension, Potency, Tactility, Spatiality and Atmosphere. Correlations between corresponding sets of factor scores were significant. On balance, the French semantic space is more complex and more sophisticated.

Lateral Organization in Pictures and Aesthetic Preference: IV. Construction with Original vs Mirror-Image Elements

Six pictures by Western artists were selected from a group of 10 reproduced as sets of transparent component overlays. For each work university students, 34 women and 16 men, were presented with one set of disassembled overlays, all either in original orientation or all laterally reversed. Their task was to select that assemblage of elements which created the best picture. Subjects' constructions confirmed that in each picture there is a constancy of structure that is independent of lateral organization. This fact coexists with whatever differential effects eliminating a component may achieve as a function of picture orientation. Pictures differ, it is suggested: (a) in the distribution of contributions which individual components make to the organization of the work and (b) in their resistance to fragmentation. Lateral elements in particular are expendable. Susceptibility to fragmentation is greater for mirror-image than original representations.

Lateral Displacement of Pictures and Best View: Is there an Artist-Specific Effect?

University Ss, 22 men and 28 women, moved pictures along the lateral axis to locate the optimum viewing position for each. The results did not support Schlesinger's claim that the effect of lateral displacement on picture unification is artist-specific.

Perceptual conflict and alcoholics

30 unselected Ss, outpatients in a clinic for alcoholics, served in a visual-recognition experiment. Positive and negative photographs of common non-motivating objects were shown under time-controlled conditions of exposure. Alcoholics as normals showed that negatives are more difficult to recognize (required a longer exposure to produce recognition) than positives and that this difference increases as a function of difficulty or object complexity. The data also suggest, however, that alcoholics are absolutely and relatively less able to process conflicting visual information than normals. The latter finding led to the hypothesis that alcohol may serve to relieve sensory discordance for the alcoholic.

Lateral organization in pictures and aesthetic preference

416 Ss, drawn with equal sex representation from Grades 1 through university level, rendered aesthetic preferences for original vs mirror-image views of each of a series of 20 pictures. The grand mean number of original views selected was significantly greater than chance expectation. Preference for the original varied significantly over pictures, with the following properties of lateral organization emerging most distinctly as influential in the response: (a) pattern of lighting, (b) profile orientation, (c) handedness characteristics, (d) quadrant distribution of important objects, and (e) ease of entering the picture space. Choice was also a function of the positional arrangement of the two views. In respect of individual differences, when preference behavior is averaged over paintings, educational level is a more important dimension than either sex or handedness. When preference is considered for paintings singly, the influence of sex and handedness may be considerable.