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Shrestha S, Tung J, Grinshpon RD, Swartz P, Hamilton PT, Dimos B, Mydlarz L, Clark AC. Caspases from scleractinian coral show unique regulatory features. J Biol Chem 2020; 295:14578-14591. [PMID: 32788218 PMCID: PMC7586219 DOI: 10.1074/jbc.ra120.014345] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/04/2020] [Indexed: 12/11/2022] Open
Abstract
Coral reefs are experiencing precipitous declines around the globe with coral diseases and temperature-induced bleaching being primary drivers of these declines. Regulation of apoptotic cell death is an important component in the coral stress response. Although cnidaria are known to contain complex apoptotic signaling pathways, similar to those in vertebrates, the mechanisms leading to cell death are largely unexplored. We identified and characterized two caspases each from Orbicella faveolata, a disease-sensitive reef-building coral, and Porites astreoides, a disease-resistant reef-building coral. The caspases are predicted homologs of the human executioner caspases-3 and -7, but OfCasp3a (Orbicella faveolata caspase-3a) and PaCasp7a (Porites astreoides caspase-7a), which we show to be DXXDases, contain an N-terminal caspase activation/recruitment domain (CARD) similar to human initiator/inflammatory caspases. OfCasp3b (Orbicella faveolata caspase-3b) and PaCasp3 (Porites astreoides caspase-3), which we show to be VXXDases, have short pro-domains, like human executioner caspases. Our biochemical analyses suggest a mechanism in coral which differs from that of humans, where the CARD-containing DXXDase is activated on death platforms but the protease does not directly activate the VXXDase. The first X-ray crystal structure of a coral caspase, of PaCasp7a determined at 1.57 Å resolution, reveals a conserved fold and an N-terminal peptide bound near the active site that may serve as a regulatory exosite. The binding pocket has been observed in initiator caspases of other species. These results suggest mechanisms for the evolution of substrate selection while maintaining common activation mechanisms of CARD-mediated dimerization.
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Affiliation(s)
- Suman Shrestha
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
| | - Jessica Tung
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
| | - Robert D Grinshpon
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Paul Swartz
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Paul T Hamilton
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Bradford Dimos
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
| | - Laura Mydlarz
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
| | - A Clay Clark
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA.
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Agarwal S, Smith M, De La Rosa I, Verba KA, Swartz P, Segura-Totten M, Mattos C. Development of a structure-analysis pipeline using multiple-solvent crystal structures of barrier-to-autointegration factor. Acta Crystallogr D Struct Biol 2020; 76:1001-1014. [DOI: 10.1107/s2059798320011341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 08/18/2020] [Indexed: 11/10/2022] Open
Abstract
The multiple-solvent crystal structure (MSCS) approach uses high concentrations of organic solvents to characterize the interactions and effects of solvents on proteins. Here, the method has been further developed and an MSCS data-handling pipeline is presented that uses the Detection of Related Solvent Positions (DRoP) program to improve data quality. DRoP is used to selectively model conserved water molecules, so that an advanced stage of structural refinement is reached quickly. This allows the placement of organic molecules more accurately and convergence on high-quality maps and structures. This pipeline was applied to the chromatin-associated protein barrier-to-autointegration factor (BAF), resulting in structural models with better than average statistics. DRoP and Phenix Structure Comparison were used to characterize the data sets and to identify a binding site that overlaps with the interaction site of BAF with emerin. The conserved water-mediated networks identified by DRoP suggested a mechanism by which water molecules are used to drive the binding of DNA. Normalized and differential B-factor analysis is shown to be a valuable tool to characterize the effects of specific solvents on defined regions of BAF. Specific solvents are identified that cause stabilization of functionally important regions of the protein. This work presents tools and a standardized approach for the analysis and comprehension of MSCS data sets.
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Kearney BM, Schwabe M, Marcus KC, Roberts DM, Dechene M, Swartz P, Mattos C. DRoP: Automated detection of conserved solvent-binding sites on proteins. Proteins 2019; 88:152-165. [PMID: 31294888 DOI: 10.1002/prot.25781] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 06/19/2019] [Accepted: 07/06/2019] [Indexed: 11/08/2022]
Abstract
Water and ligand binding play critical roles in the structure and function of proteins, yet their binding sites and significance are difficult to predict a priori. Multiple solvent crystal structures (MSCS) is a method where several X-ray crystal structures are solved, each in a unique solvent environment, with organic molecules that serve as probes of the protein surface for sites evolved to bind ligands, while the first hydration shell is essentially maintained. When superimposed, these structures contain a vast amount of information regarding hot spots of protein-protein or protein-ligand interactions, as well as conserved water-binding sites retained with the change in solvent properties. Optimized mining of this information requires reliable structural data and a consistent, objective analysis tool. Detection of related solvent positions (DRoP) was developed to automatically organize and rank the water or small organic molecule binding sites within a given set of structures. It is a flexible tool that can also be used in conserved water analysis given multiple structures of any protein independent of the MSCS method. The DRoP output is an HTML format list of the solvent sites ordered by conservation rank in its population within the set of structures, along with renumbered and recolored PDB files for visualization and facile analysis. Here, we present a previously unpublished set of MSCS structures of bovine pancreatic ribonuclease A (RNase A) and use it together with published structures to illustrate the capabilities of DRoP.
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Affiliation(s)
- Bradley M Kearney
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts.,Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina
| | - Michael Schwabe
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Kendra C Marcus
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Daniel M Roberts
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina
| | - Michelle Dechene
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina
| | - Paul Swartz
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts.,Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina
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Clark C, Shrestha S, Tung J, Swartz P, Grinshpon R, Mydlarz L. Caspases from Scleractinian coral show unique regulatory features. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.779.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Clay Clark
- BiologyUniversity of Texas at ArlingtonArlingtonTX
| | | | - Jussica Tung
- BiologyUniversity of Texas at ArlingtonArlingtonTX
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Thomas ME, Grinshpon R, Swartz P, Clark AC. Modifications to a common phosphorylation network provide individualized control in caspases. J Biol Chem 2018; 293:5447-5461. [PMID: 29414778 DOI: 10.1074/jbc.ra117.000728] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/24/2018] [Indexed: 11/06/2022] Open
Abstract
Caspase-3 activation and function have been well-defined during programmed cell death, but caspase activity, at low levels, is also required for developmental processes such as lymphoid proliferation and erythroid differentiation. Post-translational modification of caspase-3 is one method used by cells to fine-tune activity below the threshold required for apoptosis, but the allosteric mechanism that reduces activity is unknown. Phosphorylation of caspase-3 at a conserved allosteric site by p38-MAPK (mitogen-activated protein kinase) promotes survival in human neutrophils, and the modification of the loop is thought to be a key regulator in many developmental processes. We utilized phylogenetic, structural, and biophysical studies to define the interaction networks that facilitate the allosteric mechanism in caspase-3. We show that, within the modified loop, Ser150 evolved with the apoptotic caspases, whereas Thr152 is a more recent evolutionary event in mammalian caspase-3. Substitutions at Ser150 result in a pH-dependent decrease in dimer stability, and localized changes in the modified loop propagate to the active site of the same protomer through a connecting surface helix. Likewise, a cluster of hydrophobic amino acids connects the conserved loop to the active site of the second protomer. The presence of Thr152 in the conserved loop introduces a "kill switch" in mammalian caspase-3, whereas the more ancient Ser150 reduces without abolishing enzyme activity. These data reveal how evolutionary changes in a conserved allosteric site result in a common pathway for lowering activity during development or a more recent cluster-specific switch to abolish activity.
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Affiliation(s)
- Melvin E Thomas
- From the Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27608 and
| | - Robert Grinshpon
- From the Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27608 and
| | - Paul Swartz
- From the Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27608 and
| | - A Clay Clark
- the Department of Biology, University of Texas, Arlington, Texas 76019
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Kantor JR, Kelton JD, Cardno JA, Wilder JL, Mountjoy PT, Swartz P, Honig WK, Layman EM, Pronko NH. Book Reviews. Psychol Rec 2017. [DOI: 10.1007/bf03393509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Swartz P. Perspectives in psychology. Psychol Rec 2017. [DOI: 10.1007/bf03393302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Tucker MB, MacKenzie SH, Maciag JJ, Dirscherl Ackerman H, Swartz P, Yoder JA, Hamilton PT, Clay Clark A. Phage display and structural studies reveal plasticity in substrate specificity of caspase-3a from zebrafish. Protein Sci 2016; 25:2076-2088. [PMID: 27577093 PMCID: PMC5079243 DOI: 10.1002/pro.3032] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 08/02/2016] [Accepted: 08/25/2016] [Indexed: 01/27/2023]
Abstract
The regulation of caspase-3 enzyme activity is a vital process in cell fate decisions leading to cell differentiation and tissue development or to apoptosis. The zebrafish, Danio rerio, has become an increasingly popular animal model to study several human diseases because of their transparent embryos, short reproductive cycles, and ease of drug administration. While apoptosis is an evolutionarily conserved process in metazoans, little is known about caspases from zebrafish, particularly regarding substrate specificity and allosteric regulation compared to the human caspases. We cloned zebrafish caspase-3a (casp3a) and examined substrate specificity of the recombinant protein, Casp3a, compared to human caspase-3 (CASP3) by utilizing M13 bacteriophage substrate libraries that incorporated either random amino acids at P5-P1' or aspartate fixed at P1. The results show a preference for the tetrapeptide sequence DNLD for both enzymes, but the P4 position of zebrafish Casp3a also accommodates valine equally well. We determined the structure of zebrafish Casp3a to 2.28Å resolution by X-ray crystallography, and when combined with molecular dynamics simulations, the results suggest that a limited number of amino acid substitutions near the active site result in plasticity of the S4 sub-site by increasing flexibility of one active site loop and by affecting hydrogen-bonding with substrate. The data show that zebrafish Casp3a exhibits a broader substrate portfolio, suggesting overlap with the functions of caspase-6 in zebrafish development.
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Affiliation(s)
- Matthew B Tucker
- Department of Molecular and Structural Biochemistry, NC State University, Raleigh, North Carolina, 27608
| | - Sarah H MacKenzie
- Department of Molecular and Structural Biochemistry, NC State University, Raleigh, North Carolina, 27608
| | - Joseph J Maciag
- Department of Molecular and Structural Biochemistry, NC State University, Raleigh, North Carolina, 27608
| | | | - Paul Swartz
- Department of Molecular and Structural Biochemistry, NC State University, Raleigh, North Carolina, 27608
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, NC State University, Raleigh, North Carolina, 27608
| | - Paul T Hamilton
- Department of Plant and Microbial Biology, NC State University, Raleigh, North Carolina, 27608
| | - A Clay Clark
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019.
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Abstract
A group of 60 university students, 30 men and 30 women, completed Hood's Mysticism Scale, Research Form D (M Scale) and performed a motor skills task following body rotation. Subjects with the strongest tendency to mystical experience exhibited least destability, although only for the women was the association statistically significant. Women as a group scored higher on the M Scale and performed better in the motor skills task.
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Abstract
Personal myth is the individual aesthetic resolution of our experience of being present in the world in both a particulate and transcendent way. Beginning early, personal myth develops as the core of our individual psychological nature and the foundation of our personal view of reality. The evolution of transcendent encounter into a continuous present experience fixes the pattern of the duality of our existence and initiates the personal mythmaking process. Myth bridges the particulate and transcendent realms by combining selected sets of transcendent properties into idealized particulate images. The act retains the archetypal values appropriate to the parent transcendent encounters. These values supply the story the myth tells. Personal myth operates in the particulate realm to condition the way we transact the world's business. In the transcendent realm it enhances the symbolic value of events to make them available as media of self-instruction.
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Abstract
Two fundamental modes of human-being-in-the-world are distinguished. In the particulate mode engagement is with objects in their specificity. In the transcendent mode, which establishes the person in phenomenal union with the world, transactions are with qualities and conditions qua qualities and conditions. To each mode a distinctive field-character attaches, differing in the elements of articulatedness, continuity, and in the logic of event inclusion. Knowing in the transcendent mode is of oneness and proceeds through immediate apprehension. Certain transcendent encounters are in their possibility ontological in nature. Such define the compass of universal human experience. Interpretable as transcendent transactions are Maslow's “peak-experience” and Buber's “I-Thou” encounter.
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Abstract
Self-realization, like music, images time. But whereas music images lived time, self-realization images the virtual time particular to personal myth. In the well-lived life the sense of eternal return native to personal myth becomes an awareness of continual, richening return to what we now are and always have been. The recurrence transtemporalizes us, raising the life course into a living work of art.
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Abstract
In the continuous present we experience an interior succession, in which contact is with qualities and conditions qua qualities and conditions and not as localized in the thing or event that bears them. Events arise successively, but the succession is a sequence of contiguous re-creations through which as an enlargement of the present there slowly emerges a unified impression. Gertrude Stein erected an equivalent movement into a principle of literary composition. Viewed within J. W. Dunne's serial perspective, the continuous present arises when our habitual, three-dimensional present is incompletely replaced by a four-dimensional, enlarged present. If, as Norman Brown's psychoanalytic hypothesis asserts, time has its origin in the dynamics of repression, or if, following Dunne, it is habit that maintains us in a contracted present, raising these mechanisms should lengthen our experiences of the continuous present.
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Abstract
Psychologically considered, the art of any given period defines an array of sensibilities imaginatively translated into patterns of sharable experience. These configurations have scientific value not as samples of life but as indices of the advancing edge of man's collective participation in the world. Psychology and literature meet not at the level of data but of myth, at the fons et origo of artistic creation. What the artist has to communicate to the scientist is the metaphysical principle of his works. Distilled and made the focus of scientific study, such material can open windows on man's evolving universal life.
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Abstract
10 pictures by Western artists were reproduced as sets of transparent component overlays. For each work, University Ss, 37 women and 17 men, first rendered aesthetic preferences for original vs mirror-image views. Ss then disassembled the two views, and by restoring corresponding components, worked to achieve a partial representation in which the initially non-preferred view became the preferred one. The data allow certain extensions and refinements of conclusions from earlier studies in this series: I. The normal effect of promoting liking for a view exercised by a principal mass in the lower left quadrant may be reversed if the object is present beyond a certain level of prominence. II. Ease of entering the picture space may for some persons be more determinative of aesthetic value than the distribution of principal masses. III. Lines and contours consistent with the path of glance ease entry into the picture space, hence, promote liking for a view. Consistency may, however, be excessive, and the effect on liking may reverse.
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Abstract
University Ss, 25 men and 25 women, rendered aesthetic preferences for original vs mirror-image views of each of 12 pictures. The stimuli used allowed a prediction of liking for 6 originals and 6 reversals. Prediction was based on the following properties of lateral organization: (a) pattern of lighting, (b) profile orientation, (c) handedness characteristics, (d) quadrant distribution of important objects, and (e) ease of entering the picture space. Two predictions were confirmed, while no differences in the opposite direction achieved significance. In a supplemental study with 18 boys and 20 girls in fourth grade, only one prediction was sustained, but this replicated a confirmation for the older Ss. Again, no differences in the nonpredicted direction reached significance. The results encourage expanded study.
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Abstract
University Ss, 48 men and 48 women, rendered judgments of Michelangelo's Pietàs. The instrument used was a 40-scale form of the semantic differential. Alpha factoring, based on the mean ratings for all Ss, and varimax rotation was performed for scales as variables. Seven factors emerged, in order: form, receptiveness, activity, affectivity, potency, reality and spirituality. Ss judged the earliest work to be structurally the most elegant, to incorporate the greatest receptiveness, to be most transcendent, most spiritual, and to be least active. They judged the last to be least elegant, to incorporate the least strength, the least receptiveness, to be least tragic, and least spiritual.
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Abstract
Caspases have several allosteric sites that bind small molecules or peptides. Allosteric regulators are known to affect caspase enzyme activity, in general, by facilitating large conformational changes that convert the active enzyme to a zymogen-like form in which the substrate-binding pocket is disordered. Mutations in presumed allosteric networks also decrease activity, although large structural changes are not observed. Mutation of the central V266 to histidine in the dimer interface of caspase-3 inactivates the enzyme by introducing steric clashes that may ultimately affect positioning of a helix on the protein surface. The helix is thought to connect several residues in the active site to the allosteric dimer interface. In contrast to the effects of small molecule allosteric regulators, the substrate-binding pocket is intact in the mutant, yet the enzyme is inactive. We have examined the putative allosteric network, in particular the role of helix 3, by mutating several residues in the network. We relieved steric clashes in the context of caspase-3(V266H), and we show that activity is restored, particularly when the restorative mutation is close to H266. We also mimicked the V266H mutant by introducing steric clashes elsewhere in the allosteric network, generating several mutants with reduced activity. Overall, the data show that the caspase-3 native ensemble includes the canonical active state as well as an inactive conformation characterized by an intact substrate-binding pocket, but with an altered helix 3. The enzyme activity reflects the relative population of each species in the native ensemble.
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Affiliation(s)
- Christine Cade
- Department of Molecular and Structural Biochemistry and ‡Center for Comparative Medicine and Translational Research, North Carolina State University , Raleigh, North Carolina 27695, United States
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Kearney BM, Johnson CW, Roberts DM, Swartz P, Mattos C. DRoP: a water analysis program identifies Ras-GTP-specific pathway of communication between membrane-interacting regions and the active site. J Mol Biol 2013; 426:611-29. [PMID: 24189050 DOI: 10.1016/j.jmb.2013.10.036] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 10/26/2013] [Accepted: 10/28/2013] [Indexed: 01/09/2023]
Abstract
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.
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Affiliation(s)
- Bradley M Kearney
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA; Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Christian W Johnson
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Daniel M Roberts
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Paul Swartz
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA; Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA.
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MacKenzie SH, Schipper JL, England EJ, Thomas ME, Blackburn K, Swartz P, Clark AC. Lengthening the intersubunit linker of procaspase 3 leads to constitutive activation. Biochemistry 2013; 52:6219-31. [PMID: 23941397 DOI: 10.1021/bi400793s] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
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.
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Affiliation(s)
- Sarah H MacKenzie
- Department of Molecular and Structural Biochemistry and ‡Center for Comparative Medicine and Translational Research, North Carolina State University , Raleigh, North Carolina 27695, United States
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Walters J, Swartz P, Mattos C, Clark AC. Thermodynamic, enzymatic and structural effects of removing a salt bridge at the base of loop 4 in (pro)caspase-3. Arch Biochem Biophys 2011; 508:31-8. [PMID: 21266160 DOI: 10.1016/j.abb.2011.01.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 01/14/2011] [Accepted: 01/15/2011] [Indexed: 12/31/2022]
Abstract
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.
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Affiliation(s)
- Jad Walters
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, USA
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Abstract
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.
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Affiliation(s)
- Michelle Dechene
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
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Subbiah SKV, Moe J, Desai D, Holzapfel GA, Wink G, Swartz P, Mattos C. Multiple Solvent Crystal Structures of Chymotrypsin: Comparision with Elastase. FASEB J 2007. [DOI: 10.1096/fasebj.21.5.a639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Jonathan Moe
- Molecular & Structural BiochemistryNorth Carolina State University128 Polk HallRaleighNC27695
| | - Divya Desai
- Molecular & Structural BiochemistryNorth Carolina State University128 Polk HallRaleighNC27695
| | | | - Glenna Wink
- Molecular & Structural BiochemistryNorth Carolina State University128 Polk HallRaleighNC27695
| | - Paul Swartz
- Molecular & Structural BiochemistryNorth Carolina State University128 Polk HallRaleighNC27695
| | - Carla Mattos
- Molecular & Structural BiochemistryNorth Carolina State University128 Polk HallRaleighNC27695
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Dechene MC, Wink G, Cholewa C, Swartz P, Mattos C. Multiple solvent crystal structures of RNAse A. FASEB J 2007. [DOI: 10.1096/fasebj.21.6.a1010-c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Michelle C Dechene
- Department of Molecular and Structural BiochemistryNorth Carolina State University128 Polk Hall; Box 7622RaleighNC27695‐7622
| | - Glenna Wink
- Department of Molecular and Structural BiochemistryNorth Carolina State University128 Polk Hall; Box 7622RaleighNC27695‐7622
| | - Crystal Cholewa
- Department of Molecular and Structural BiochemistryNorth Carolina State University128 Polk Hall; Box 7622RaleighNC27695‐7622
| | - Paul Swartz
- Department of Molecular and Structural BiochemistryNorth Carolina State University128 Polk Hall; Box 7622RaleighNC27695‐7622
| | - Carla Mattos
- Department of Molecular and Structural BiochemistryNorth Carolina State University128 Polk Hall; Box 7622RaleighNC27695‐7622
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Abstract
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.
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Affiliation(s)
| | | | | | | | - A. Clay Clark
- To whom correspondence should be addressed: Department of Molecular and Structural Biochemistry, 128 Polk Hall, North Carolina State University, Raleigh, NC 27695-7622. Phone: (919) 515-5805. Fax: (919) 515-2047.
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Palmer SM, Swartz P, Mattos C. Comparison between experimental Multiple Solvent Crystal Structures and Computational Solvent Mapping of Hen Eggwhite Lysozyme. FASEB J 2006. [DOI: 10.1096/fasebj.20.4.a476-b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Shawn Michelle Palmer
- Molecular and Structural BiochemistryNorth Carolina State University423 Appledown DrCaryNC27513
| | - Paul Swartz
- Molecular and Structural BiochemistryNorth Carolina State University, 128 Polk HallNorth Carolina State UniversityRaleighNC27695
| | - Carla Mattos
- Molecular and Structural BiochemistryNorth Carolina State University114 E. Park Dr.RaleighNC27605
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Abstract
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.
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Swartz P. Contributions to the history of psychology: XLVII. Ignatius Loyola and behavior therapy. Percept Mot Skills 1988; 66:617-8. [PMID: 3041366 DOI: 10.2466/pms.1988.66.2.617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
An early instance of what we call behavior therapy, devised by Ignatius Loyola, is noted.
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Affiliation(s)
- P Swartz
- Department of Psychology, University of Alberta, Edmonton, Canada
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Abstract
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.
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Affiliation(s)
- P Swartz
- Department of Psychology, University of Alberta, Edmonton, Canada
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Swartz P, Madison G. Contributions to Psychohistory: XII. the View from Betwixt and Between: J. M. Barrie and Humankind. Percept Mot Skills 1987. [DOI: 10.2466/pms.1987.65.1.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
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.
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Abstract
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.
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Swartz P. Effect of Face-Masking on Aesthetic Judgment. Percept Mot Skills 1980. [DOI: 10.2466/pms.1980.51.1.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
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.
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Abstract
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.
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Abstract
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.
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Abstract
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.
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Swartz P, Swartz S. Lateral Organization in Pictures and Aesthetic Preference: IV. Construction with Original vs Mirror-Image Elements. Percept Mot Skills 1976. [DOI: 10.2466/pms.1976.42.3c.1023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
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.
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Swartz P, Collier G, Swartz S. Lateral Displacement of Pictures and Best View: Is there an Artist-Specific Effect? Percept Mot Skills 1974. [DOI: 10.2466/pms.1974.39.1.343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
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.
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Abstract
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.
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Abstract
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.
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Dashiell JF, Pronko NH, Lichtenstein PE, Swartz P, Honig WK. Book reviews. Psychol Rec 1962. [DOI: 10.1007/bf03393447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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