The Individual Domain

Filamins are large proteins that cross-link actin filaments and connect to other cellular components. The C-terminal rod 2 region of FLNa (filamin A) mediates dimerization and interacts with several transmembrane receptors and intracellular signalling adaptors. SAXS (small-angle X-ray scattering) experiments were used to make a model of a six immunoglobulin-like domain fragment of the FLNa rod 2 (domains 16–21). This fragment had a surprising three-branched structural arrangement, where each branch was made of a tightly packed two-domain pair. Peptides derived from transmembrane receptors and intracellular signalling proteins induced a more open structure of the six domain fragment. Mutagenesis studies suggested that these changes are caused by peptides binding to the CD faces on domains 19 and 21 which displace the preceding domain A-strands (18 and 20 respectively), thus opening the individual domain pairs. A single particle cryo-EM map of a nine domain rod 2 fragment (domains 16–24), showed a relatively compact dimeric particle and confirmed the three-branched arrangement as well as the peptide-induced conformation changes. These findings reveal features of filamin structure that are important for its interactions and mechanical properties.

Download Full-text

Persistent homology analysis of deconfinement transition in effective Polyakov-line model

International Journal of Modern Physics A ◽

10.1142/s0217751x20500499 ◽

2020 ◽

Vol 35 (10) ◽

pp. 2050049

Author(s):

Takehiro Hirakida ◽

Kouji Kashiwa ◽

Junpei Sugano ◽

Junichi Takahashi ◽

Hiroaki Kouno ◽

...

Keyword(s):

Persistent Homology ◽

Rectangular Lattice ◽

Spatial Average ◽

Lattice Data ◽

Line Model ◽

Data Space ◽

Homology Analysis ◽

Individual Domain ◽

The Individual ◽

Polyakov Line

The persistent homology analysis is applied to the effective Polyakov-line model on a rectangular lattice to investigate the confinement–deconfinement nature. The lattice data are mapped onto the complex Polyakov-line plane without taking the spatial average and then the plane is divided into three domains. This study is based on previous studies for the clusters and the percolation properties in lattice QCD, but the mathematical method of the analyses are different. The spatial distribution of the data in the individual domain is analyzed by using the persistent homology to obtain information of the multiscale structure of center clusters. In the confined phase, the data in the three domains show the same topological tendency characterized by the birth and death times of the holes which are estimated via the filtration of the alpha complexes in the data space, but do not in the deconfined phase. By considering the configuration averaged ratio of the birth and death times of holes, we can construct the nonlocal order parameter of the confinement–deconfinement transition from the multiscale topological properties of center clusters.

Download Full-text

Terminal short arm domains of basement membrane laminin are critical for its self-assembly.

The Journal of Cell Biology ◽

10.1083/jcb.110.3.825 ◽

1990 ◽

Vol 110 (3) ◽

pp. 825-832 ◽

Cited By ~ 77

Author(s):

J C Schittny ◽

P D Yurchenco

Keyword(s):

Self Assembly ◽

Affinity Column ◽

Dependent Manner ◽

Concentration Dependent Manner ◽

Calcium Dependent ◽

Domain Specific ◽

Binding Domains ◽

Individual Domain ◽

The Individual

Laminin self-assembles into large polymers by a cooperative two-step calcium-dependent mechanism (Yurchenco, P. D., E. C. Tsilibary, A. S. Charonis, and H. Furthmayr. 1985. J. Biol. Chem. 260:7636-7644). The domain specificity of this process was investigated using defined proteolytically generated fragments corresponding to the NH2-terminal globule and adjacent stem of the short arm of the B1 chain (E4), a complex of the two short arms of the A and B2 chains attached to the proximal stem of a third short arm (E1'), a similar complex lacking the globular domains (P1'), and the distal half of the long arm attached to the adjacent portion of the large globule (E8). Polymerization, followed by an increase of turbidity at 360 nm in neutral isotonic TBS containing CaCl2 at 35 degrees C, was quantitatively inhibited in a concentration-dependent manner with laminin fragments E4 and E1' but not with fragments E8 and P1'. Affinity retardation chromatography was used for further characterization of the binding of laminin domains. The migration of fragment E4, but not of fragments E8 and P1', was retarded in a temperature- and calcium-dependent fashion on a laminin affinity column but not on a similar BSA column. These data are evidence that laminin fragments E4 and E1' possess essential terminal binding domains for the self-aggregation of laminin, while fragments E8 and P1' do not. Furthermore, the individual domain-specific interactions that contribute to assembly are calcium dependent and of low affinity.

Download Full-text

Musical creativity and the embodied mind

Music & Science ◽

10.1177/2059204318792319 ◽

2018 ◽

Vol 1 ◽

pp. 205920431879231 ◽

Cited By ~ 12

Author(s):

Dylan van der Schyff ◽

Andrea Schiavio ◽

Ashley Walton ◽

Valerio Velardo ◽

Anthony Chemero

Keyword(s):

Cognitive Process ◽

Future Research ◽

Embodied Interaction ◽

Wide Range ◽

Recent Developments ◽

Individual Domain ◽

Embodied Cognitive Science ◽

Musical Creativity ◽

Temporal Dimensions ◽

The Individual

The phenomenon of creativity has received a growing amount of attention from scholars working across a range of disciplines. While this research has produced many important insights, it has also traditionally tended to explore creativity in terms of the reception of products or outcomes, conceiving of it as a cognitive process that is limited to the individual domain of the creative agent. More recently, however, researchers have begun to develop perspectives on creativity that highlight the patterns of adaptive embodied interaction that occur between multiple agents, as well as the broader socio-material milieu they are situated in. This has promoted new understandings of creativity, which is now often considered as a distributed phenomenon. Because music involves such a wide range of socio-cultural, bodily, technological, and temporal dimensions it is increasingly taken as a paradigmatic example for researchers who wish to explore creativity from this more relational perspective. In this article, we aim to contribute to this project by discussing musical creativity in light of recent developments in embodied cognitive science. More specifically, we will attempt to frame an approach to musical creativity based in an 4E (embodied, embedded, enactive, and extended) understanding of cognition. We suggest that this approach may help us better understand creativity in terms of how interacting individuals and social groups bring forth worlds of meaning through shared, embodied processes of dynamic interactivity. We also explore how dynamical systems theory (DST) may offer useful tools for research and theory that align closely with the 4E perspective. To conclude, we summarize our discussion and suggest possibilities for future research.

Download Full-text

Case-Based Expert System to Support Electronics Design in Mechatronic System

Applied Mechanics and Materials ◽

10.4028/www.scientific.net/amm.229-231.2793 ◽

2012 ◽

Vol 229-231 ◽

pp. 2793-2797

Author(s):

Samir El-Nakla

Keyword(s):

Expert System ◽

Design Process ◽

Mechatronic System ◽

Mechatronic Systems ◽

Overall Design ◽

Individual Domain ◽

Access Information ◽

The Individual ◽

Current Systems ◽

Case Based

Many current systems rely for their performance on achieving a balance between electronics, software and mechanical systems and the transfer of functionality between those domains. The design of such mechatronic systems therefore relies on the ability of the individual domain specialists to transfer knowledge about their domain within the overall design process. Enhancing the ability of non-specialists to understand the relationships between the various system elements and to communicate with the domain specialists will serve to enhance and support the design process. The paper therefore considers a tool based around the use of case-based expert system which is intended to provide such support by allowing a non-specialist to access information from a range of domains in a way which is easy to use and understand and which will establish and define the links between the various areas of technology.

Download Full-text

ProtCID: A data resource for structural information on protein interactions

10.1101/579862 ◽

2019 ◽

Cited By ~ 1

Author(s):

Qifang Xu ◽

Roland L. Dunbrack

Keyword(s):

Nucleic Acids ◽

Protein Interactions ◽

Structural Information ◽

Large Protein ◽

Data Resource ◽

Protein Clusters ◽

Individual Domain ◽

Common Interface ◽

The Individual ◽

Domain Level

AbstractStructural information on the interactions of proteins with other molecules is plentiful, and for some proteins and protein families, there may be 100s of available structures. It can be very difficult for a scientist who is not trained in structural bioinformatics to access this information comprehensively. Previously, we developed the Protein Common Interface Database (ProtCID), which provided clusters of the interfaces of full-length protein chains as a means of identifying biological assemblies. Because proteins consist of domains that act as modular functional units, we have extended the analysis in ProtCID to the individual domain level. This has greatly increased the number of large protein-protein clusters in ProtCID, enabling the generation of hypotheses on the structures of biological assemblies of many systems. The analysis of domain families allows us to extend ProtCID to the interactions of domains with peptides, nucleic acids, and ligands. ProtCID provides complete annotations and coordinate sets for every cluster.

Download Full-text

Effects of electrostatic interactions on global folding and local conformational dynamics of a multidomain Y-family DNA polymerase

Physical Chemistry Chemical Physics ◽

10.1039/d1cp02832d ◽

2021 ◽

Author(s):

Qing-Miao Nie ◽

Li-Zhen Sun ◽

Hai-Bin Li ◽

Xiakun Chu ◽

Jin Wang

Keyword(s):

Dna Binding ◽

Dna Polymerase ◽

Electrostatic Interactions ◽

Conformational Dynamics ◽

Individual Domain ◽

The Individual ◽

Y Family

Electrostatic interactions can facilitate the folding of the multidomain DNA polymerase Dpo4 by refining the folding order of the individual domain and promote the functional conformational dynamics of Dpo4 during the DNA-binding recognition.

Download Full-text

A Variational Model of Ferroelectric Microstructure

Smart Materials, Adaptive Structures and Intelligent Systems, Volume 1 ◽

10.1115/smasis2008-360 ◽

2008 ◽

Cited By ~ 1

Author(s):

J. E. Huber ◽

A. C. F. Cocks

Keyword(s):

Single Crystal ◽

Degrees Of Freedom ◽

Domain Walls ◽

Hysteresis Loops ◽

Variational Model ◽

Ferroelectric Crystal ◽

Individual Domain ◽

Thermodynamic Variables ◽

The Individual ◽

Uniaxial Compressive Stress

A simple model of the evolution of ferroelectric microstructure in single crystals is developed by using variational methods to minimize a functional based on free energy and dissipation. The thermodynamic variables in this formulation correspond to the positions of a set of domain walls within a single ferroelectric crystal. The total dissipation rate is taken to be a function of the velocities of the individual domain walls. With only two-degrees of freedom, a model of this type has sufficient richness to reproduce many of the observed features found in the single crystal response of a tetragonal ferroelectric. This includes the dielectric hysteresis, butterfly hysteresis, and the variation of the hysteresis loops under uniaxial compressive stress. Additional degrees of freedom can be used to capture multi-axiality. The model also highlights the marked differences in response that should occur when a single crystal is subjected to different boundary conditions.

Download Full-text

Temporal and propositional de se: evidence from Romanian subjunctive mood

ZAS Papers in Linguistics ◽

10.21248/zaspil.44.2006.300 ◽

2006 ◽

Vol 44 (1) ◽

pp. 55-70

Author(s):

Adrian Brasoveanu

Keyword(s):

Propositional Attitude ◽

Belief Reports ◽

Belief Report ◽

Empirical Generalization ◽

Subjunctive Mood ◽

De Se ◽

Individual Domain ◽

Centered Worlds ◽

The Individual

The paper investigates the interpretation of the Romanian subjunctive B (subjB) mood when it is embedded under the propositional attitude verb crede (believe). SubjB is analyzed as a single package of three distinct presuppositions: temporal de se, dissociation and propositional de se. I show that subjB is the temporal analogue of null PRO in the individual domain: it allows only for a de se reading. Dissociation enables us to show that subjB always takes scope over a negation embedded in a belief report. Propositional de se derives this empirical generalization. The introduction of centered propositions (generalizing centered worlds), together with propositional de se, dissociation and the belief 'introspection' principles, derives the fact that subjB belief reports (unlike their indicative counterparts) are infelicitous with embedded probabil.

Download Full-text

POLITICAL ETHICS IN BERGER DIALECTICS AGAINST THE MEANING OF POWER OF THE SOUTH NIAS DPRD MEMBERS FOR THE 2014-2019 PERIOD

JHSS (JOURNAL OF HUMANITIES AND SOCIAL STUDIES) ◽

10.33751/jhss.v5i1.3201 ◽

2021 ◽

Vol 5 (1) ◽

pp. 27-31

Author(s):

Hadirat Manao

Keyword(s):

Future Orientation ◽

Political Elites ◽

Political Ethics ◽

The South ◽

Government Bureaucracy ◽

Individual Domain ◽

The Government ◽

The Individual ◽

Practical Level

The establishment of South Nias Regency is of course accompanied by the formation of new legislatif and executive institutions to run the government. The formation of these institutions provided an opportunity for the emergence of local Nias Selatan elites to take up positions as legislators and regional heads. Reflecting from the above view, this research is a case study that focuses on developing in-depth descriptions and explanations of the meaning of the position of legislatif members in South Nias in 2014. specifically the perspective of Peter L Berger's social construction.At a practical level, this study can be a "mirror" for local political elites in South Nias to understand the political dynamics in the district more sharply and deeply, and can be considered in formulating more appropriate strategies and tactics.The method in this study uses the phenomenology approach. This approach prioritizes human existence as something that must be interpreted or interpreted. Phenomenology in this study basically seeks to uncover and describe the meaning of the position of DPRD members for competing local South Nias elites. The conclusions in this study reveal that the reality of the meaning of office is in the view of members of the South Nias DPRD, namely as a mandate, arena of contestation, and aspects of interests. The factors underlying the interest of South Nias DPRD members towards positions were formed in two spheres, namely the individual domain and the community domain. In the individual domain, their interest in the position is motivated by four factors, namely internal motivation, external motivation, skills, and goals. While in the community domain there are three factors, namely the previous orientation, current orientation, and future orientation. The motive of South Nias DPRD members in choosing to become officials in the ranks of the government bureaucracy is to become a direct actor in South Nias regional development. Being an official for members of the South Nias DPRD is important than that position held by people who do not care about the development of South Nias. If the position is held by people who do not understand the history, culture and customs of South Nias, it will be fatal.

Download Full-text