scholarly journals Structural characterization and computational analysis of PDZ domains in Monosiga brevicollis

2020 ◽  
Vol 29 (11) ◽  
pp. 2226-2244
Author(s):  
Melody Gao ◽  
Iain G. P. Mackley ◽  
Samaneh Mesbahi‐Vasey ◽  
Haley A. Bamonte ◽  
Sarah A. Struyvenberg ◽  
...  
Keyword(s):  
Structural Characterization ◽  
Computational Analysis ◽  
Pdz Domains ◽  
Monosiga Brevicollis

scholarly journals Domain Analysis and Motif Matcher (DAMM): A Program to Predict Selectivity Determinants in Monosiga brevicollis PDZ Domains Using Human PDZ Data

Molecules ◽  
2021 ◽  
Vol 26 (19) ◽  
pp. 6034
Author(s):  
Haley A. Wofford ◽  
Josh Myers-Dean ◽  
Brandon A. Vogel ◽  
Kevin Alexander Estrada Alamo ◽  
Frederick A. Longshore-Neate ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Pdz Domain ◽  
Peptide Binding ◽  
Domain Analysis ◽  
Cellular Adhesion ◽  
Pdz Domains ◽  
Cellular Targets ◽  
C Terminus ◽  
Domains Of Life ◽  
Monosiga Brevicollis

Choanoflagellates are single-celled eukaryotes with complex signaling pathways. They are considered the closest non-metazoan ancestors to mammals and other metazoans and form multicellular-like states called rosettes. The choanoflagellate Monosiga brevicollis contains over 150 PDZ domains, an important peptide-binding domain in all three domains of life (Archaea, Bacteria, and Eukarya). Therefore, an understanding of PDZ domain signaling pathways in choanoflagellates may provide insight into the origins of multicellularity. PDZ domains recognize the C-terminus of target proteins and regulate signaling and trafficking pathways, as well as cellular adhesion. Here, we developed a computational software suite, Domain Analysis and Motif Matcher (DAMM), that analyzes peptide-binding cleft sequence identity as compared with human PDZ domains and that can be used in combination with literature searches of known human PDZ-interacting sequences to predict target specificity in choanoflagellate PDZ domains. We used this program, protein biochemistry, fluorescence polarization, and structural analyses to characterize the specificity of A9UPE9_MONBE, a M. brevicollis PDZ domain-containing protein with no homology to any metazoan protein, finding that its PDZ domain is most similar to those of the DLG family. We then identified two endogenous sequences that bind A9UPE9 PDZ with <100 μM affinity, a value commonly considered the threshold for cellular PDZ–peptide interactions. Taken together, this approach can be used to predict cellular targets of previously uncharacterized PDZ domains in choanoflagellates and other organisms. Our data contribute to investigations into choanoflagellate signaling and how it informs metazoan evolution.

scholarly journals Domain Analysis and Motif Matcher (DAMM): A Program to Predict Selectivity Determinants in Monosiga brevicollis PDZ Domains Using Human PDZ Data

2021 ◽  
Author(s):  
Haley A. Wofford ◽  
Josh Myers-Dean ◽  
Brandon A. Vogel ◽  
Kevin Alexander Estrada Alamo ◽  
Frederick A. Longshore-Neate ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Pdz Domain ◽  
Peptide Binding ◽  
Domain Analysis ◽  
Cellular Adhesion ◽  
Pdz Domains ◽  
Cellular Targets ◽  
C Terminus ◽  
Domains Of Life ◽  
Monosiga Brevicollis

Choanoflagellates are single-celled eukaryotes with complex signaling pathways. They are considered the closest non-metazoan ancestors to mammals and other metazoans, and form multicellular-like states called rosettes. The choanoflagellate Monosiga brevicollis contains over 150 PDZ domains, an important peptide-binding domain in all three domains of life (Archaea, Bacteria, and Eukarya). Therefore, an understanding of PDZ domain signaling pathways in choanoflagellates may provide insight into the origins of multicellularity. PDZ domains recognize the C-terminus of target proteins and regulate signaling and trafficking pathways, as well as cellular adhesion. Here, we developed a computational program, Domain Analysis and Motif Matcher (DAMM), that predicts target specificity in choanoflagellate PDZ domains by analyzing peptide-binding cleft sequence identity as compared to human PDZ domains. We used this program, protein biochemistry, fluorescence polarization, and structural analyses to characterize the specificity of A9UPE9_MONBE, a M. brevicollis PDZ domain-containing protein with no homology to any metazoan protein, finding that its PDZ domain is most similar to those of the DLG family. We then identified two endogenous sequences that bind A9UPE9 PDZ with &amp;lt;100 M affinity, a value commonly considered the threshold for cellular PDZ-peptide interactions. Taken together, this approach can be used to predict cellular targets of previously uncharacterized PDZ domains in choanoflagellates and other organisms. Our data contributes to investigations into choanoflagellate signaling and how it informs metazoan evolution.

scholarly journals Biochemical and Structural Characterization of De Novo Designed PDZ Domains

2019 ◽  
Vol 116 (3) ◽  
pp. 320a
Author(s):  
Ernesto J. Fuentes ◽  
Young Joo Sun ◽  
Matthew Sternke ◽  
Vaitea Opuu ◽  
Nicholas Panel ◽  
...  
Keyword(s):  
Structural Characterization ◽  
De Novo ◽  
Pdz Domains

scholarly journals The evolution of non-motif selectivity determinants in Monosiga brevicollis PDZ domains

2020 ◽  
Author(s):  
Melody Gao ◽  
Iain G. P. Mackley ◽  
Samaneh Mesbahi-Vasey ◽  
Haley A. Bamonte ◽  
Sarah A. Struyvenberg ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Protein Interactions ◽  
Pdz Domain ◽  
Binding Motif ◽  
Binding Affinities ◽  
Pdz Domains ◽  
Protein Protein Interactions ◽  
Signaling Systems ◽  
Neuronal Synapses ◽  
Monosiga Brevicollis

AbstractThe evolution of signaling pathways is complex and well-studied. In particular, the emergence of animal multicellularity had a major impact on protein-protein interactions and signaling systems in eukaryotic cells. However, choanoflagellates, our closest non-metazoan ancestor, contain a number of closely related signaling and trafficking proteins and domains. In addition, because choanoflagellates can adopt a rosette-/multicellular-like state, a lot can be gained by comparing proteins involved in choanoflagellate and human signaling pathways. Here, we look at how selectivity determinants evolved in the PDZ domain. There are over 250 PDZ domains in the human proteome, which are involved in critical protein-protein interactions that result in large multimolecular complexes, e.g., in the postsynaptic density of neuronal synapses. Binding of C-terminal sequences by PDZ domains is often transient and recognition typically involves 6 residues or less, with only 2 residues specifying the binding motif. We solved high resolution crystal structures of Monosiga brevicollis PDZ domains homologous to human Dlg1 PDZ2, Dlg1 PDZ3, GIPC, and SHANK1 PDZ domains to investigate if the non-motif preferences are conserved, despite hundreds of millions of years of evolution. We also calculated binding affinities for GIPC, SHANK1, and SNX27 PDZ domains from M. brevicollis. Overall, we found that peptide selectivity is conserved between these two disparate organisms, with one exception, mbDLG-3. In addition, we identify 178 PDZ domains in the M. brevicollis proteome, including 11 new sequences, which we verified using Rosetta and homology modeling. Overall, our results provide novel insight into signaling pathways in the choanoflagellate organism.

Cluster carbonyls of the [Re6(μ3-Se)8]2+ core: synthesis, structural characterization, and computational analysis

2008 ◽  
pp. 4247 ◽  
Author(s):  
Peter J. Orto ◽  
Gary S. Nichol ◽  
Noriko Okumura ◽  
Dennis H. Evans ◽  
Ramiro Arratia-Pérez ◽  
...  
Keyword(s):  
Structural Characterization ◽  
Computational Analysis

Phase behavior of cationic and anionic surfactants at low concentrations

1992 ◽  
Vol 50 (1) ◽  
pp. 694-695
Author(s):  
E. Naranjo
Keyword(s):  
Phase Behavior ◽  
Structural Characterization ◽  
Dynamic Systems ◽  
Anionic Surfactants ◽  
Intermolecular Forces ◽  
Stable Form ◽  
Surfactant Mixtures ◽  
Low Concentrations ◽  
Cationic And Anionic Surfactants ◽  
General Method

Equilibrium vesicles, those which are the stable form of aggregation and form spontaneously on mixing surfactant with water, have never been demonstrated in single component bilayers and only rarely in lipid or surfactant mixtures. Designing a simple and general method for producing spontaneous and stable vesicles depends on a better understanding of the thermodynamics of aggregation, the interplay of intermolecular forces in surfactants, and an efficient way of doing structural characterization in dynamic systems.

New ultrastructural findings about Borrelia burgdorferi by cryofixation, negative staining, thin sectioning and scanning techniques

1990 ◽  
Vol 48 (3) ◽  
pp. 582-583
Author(s):  
S. F. Hayes ◽  
M. D. Corwin ◽  
T. G. Schwan ◽  
D. W. Dorward ◽  
W. Burgdorfer
Keyword(s):  
Lyme Disease ◽  
Borrelia Burgdorferi ◽  
Structural Characterization ◽  
Negative Staining ◽  
Low Speed ◽  
Thin Sectioning ◽  
Ultrastructural Findings

Characterization of Borrelia burgdorferi strains by means of negative staining EM has become an integral part of many studies related to the biology of the Lyme disease organism. However, relying solely upon negative staining to compare new isolates with prototype B31 or other borreliae is often unsatisfactory. To obtain more satisfactory results, we have relied upon a correlative approach encompassing a variety EM techniques, i.e., scanning for topographical features and cryotomy, negative staining and thin sectioning to provide a more complete structural characterization of B. burgdorferi.For characterization, isolates of B. burgdorferi were cultured in BSK II media from which they were removed by low speed centrifugation. The sedimented borrelia were carefully resuspended in stabilizing buffer so as to preserve their features for scanning and negative staining. Alternatively, others were prepared for conventional thin sectioning and for cryotomy using modified procedures. For thin sectioning, the fixative described by Ito, et al.

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