Disruption of collagen crosslinking during sea urchin morphogenesis

1987 ◽  
Vol 45 ◽  
pp. 786-787
Author(s):  
Jeffrey D. Hardin
Keyword(s):  
Sea Urchin ◽  
Basal Lamina ◽  
Structural Changes ◽  
Lysyl Oxidase ◽  
Three Dimensional ◽  
Specific Inhibitor ◽  
Dimensional Structure ◽  
Collagen Crosslinking ◽  
Sea Urchin Embryos ◽  
Mesenchyme Cell

The extracellular matrix (ECM) is important for many events during embryonic development. An important component of the ECM in sea urchin embryos is collagen. Collagen has been identified in the basal lamina of sea urchin embryos by morphological and immunological criteria. Recently, the need for a crosslinked collagenous matrix in the basal lamina during sea urchin embryogenesis has been demonstrated using β–aminoproprionitrile (BAPN). BAPN is a specific inhibitor of lysyl oxidase, an enzyme involved in collagen crosslinking. BAPN treatment causes completely reversible developmental arrest at the early gastrula stage, or supression of mesenchyme cell motility and archenteron elongation, depending on the time of addition of the drug. BAPN also significantly decreases the extent of collagen crosslinking, based on solubility assays. This study examines fine structural changes in cellular morphology and motility and the three-dimensional structure of the ECM induced by BAPN treatment during gastrulation and larva formation in the sea urchin embryo.

Protein intrachain contact prediction with most interacting residues (MIR)

2014 ◽  
Vol 10 (4) ◽  
Author(s):  
Ruben Acuña ◽  
Zoé Lacroix ◽  
Nikolaos Papandreou ◽  
Jacques Chomilier
Keyword(s):  
Structural Changes ◽  
Hydrophobic Interactions ◽  
Three Dimensional ◽  
Accessible Surface Area ◽  
Dimensional Structure ◽  
Closed Loops ◽  
Folding Process ◽  
Folding Nucleus ◽  
Accessible Surface ◽  
The Stability

AbstractThe transition state ensemble during the folding process of globular proteins occurs when a sufficient number of intrachain contacts are formed, mainly, but not exclusively, due to hydrophobic interactions. These contacts are related to the folding nucleus, and they contribute to the stability of the native structure, although they may disappear after the energetic barrier of transition states has been passed. A number of structure and sequence analyses, as well as protein engineering studies, have shown that the signature of the folding nucleus is surprisingly present in the native three-dimensional structure, in the form of closed loops, and also in the early folding events. These findings support the idea that the residues of the folding nucleus become buried in the very first folding events, therefore helping the formation of closed loops that act as anchor structures, speed up the process, and overcome the Levinthal paradox. We present here a review of an algorithm intended to simulate in a discrete space the early steps of the folding process. It is based on a Monte Carlo simulation where perturbations, or moves, are randomly applied to residues within a sequence. In contrast with many technically similar approaches, this model does not intend to fold the protein but to calculate the number of non-covalent neighbors of each residue, during the early steps of the folding process. Amino acids along the sequence are categorized as most interacting residues (MIRs) or least interacting residues. The MIR method can be applied under a variety of circumstances. In the cases tested thus far, MIR has successfully identified the exact residue whose mutation causes a switch in conformation. This follows with the idea that MIR identifies residues that are important in the folding process. Most MIR positions correspond to hydrophobic residues; correspondingly, MIRs have zero or very low accessible surface area. Alongside the review of the MIR method, we present a new postprocessing method called smoothed MIR (SMIR), which refines the original MIR method by exploiting the knowledge of residue hydrophobicity. We review known results and present new ones, focusing on the ability of MIR to predict structural changes, secondary structure, and the improved precision with the SMIR method.

Role of LHCII-containing macrodomains in the structure, function and dynamics of grana

2000 ◽  
Vol 27 (3) ◽  
pp. 279 ◽  
Author(s):  
G. Garab ◽  
L. Mustárdy
Keyword(s):  
Excitation Energy ◽  
Long Range ◽  
Structural Changes ◽  
Higher Plants ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Lateral Heterogeneity ◽  
Long Distance ◽  
3D Network

In higher plants and green algae two types of thylakoids are distinguished, granum (stacked) and stroma (unstacked) thylakoids. They form a three-dimensional (3D) network with large lateral heterogeneity: photosystem II (PSII) and the associated main chlorophyll a/b light-harvesting complex (LHCII) are found predominantly in the stacked region, while PSI and LHCI are located mainly in the unstacked region of the membrane. This picture emerged from the discovery of the physical separation of the two photosystems (Boardman and Anderson 1964). Granal chloroplasts possess significant flexibility, which is essential for optimizing the photosynthetic machinery under various environmental conditions. However, our understanding concerning the assembly, structural dynamics and regulatory functions of grana is far from being complete. In this paper we overview the significance of the three-dimensional structure of grana in the absorption properties, ionic equilibrations, and in the diffusion of membrane components between the stacked and unstacked regions. Further, we discuss the role of chiral macrodomains in the grana. Lateral heterogeneity of thylakoid membranes is proposed to be a consequence of the formation of macrodomains constituted of LHCII and PSII; their long range order permits long distance migration of excitation energy, which explains the energetic connectivity of PSII particles. The ability of macrodomains to undergo light-induced reversible structural changes lends structural flexibility to the granum. In purified LHCII, which has also been shown to form stacked lamellar aggregates with long range chiral order, excitation energy migrates for large distances; these macroaggregates are also capable of undergoing light-induced reversible structural changes and fluorescence quenching. Hence, some basic properties of grana appear to originate from its main constituent, the LHCII.

Structure of the Calcium Pump from Sarcoplasmic Reticulum at 8 Å Resolution: Architecture of the Transmembrane Helices and Localization of the Binding Site for Thapsigargin

1998 ◽  
Vol 4 (S2) ◽  
pp. 462-463
Author(s):  
P. Zhang ◽  
C. Toyoshima ◽  
K. Yonekura ◽  
G. Inesi ◽  
M. Green ◽  
...  
Keyword(s):  
Sarcoplasmic Reticulum ◽  
Transmembrane Domain ◽  
Three Dimensional ◽  
Specific Inhibitor ◽  
Large Family ◽  
Calcium Pump ◽  
Dimensional Structure ◽  
Transmembrane Helices ◽  
Site Mutagenesis ◽  
P Type

The calcium pump (Ca2+-ATPase) from sarcoplasmic reticulum (SR) is a prominent member of the large family of ATP-dependent cation pumps, which include Na+ /K+-ATPase, H+/K+-ATPase from the stomach, H+-ATPase from yeast and Neurospora, and various detoxifying pumps for Cd+, Cu+ and other metals. In muscle, calcium is stored inside the SR and contraction is initiated by regulated release through specific calcium channels; Ca2+ -ATPase is responsible for relaxation by pumping calcium back into the SR lumen. Many techniques (chemical modification, site mutagenesis, reaction kinetics) have been used to correlate Ca2+-ATPase sequence with function, but no high resolution three-dimensional structure of Ca2+-ATPase, or any P-type pump, has yet been determined. In the current work, we have determined the structure from helical crystals at 8 A resolution and thus revealed the alpha-helical architecture of the transmembrane domain. In addition, a specific inhibitor of Ca2+-ATPase, thapsigargin, was used to promote crystallization and we have characterized the structural consequences of its inhibition.

scholarly journals Evidence for a Conformational Change in Actin Induced by Fimbrin (N375) Binding

1997 ◽  
Vol 139 (2) ◽  
pp. 387-396 ◽  
Author(s):  
Dorit Hanein ◽  
Paul Matsudaira ◽  
David J. DeRosier
Keyword(s):  
Actin Filaments ◽  
Structural Changes ◽  
Three Dimensional ◽  
Binding Domain ◽  
Actin Binding ◽  
Dimensional Structure ◽  
Binding Surface ◽  
Actin Binding Domain ◽  
Actin Structure ◽  
Signal Transduction Proteins

Fimbrin belongs to a superfamily of actin cross-linking proteins that share a conserved 27-kD actin-binding domain. This domain contains a tandem duplication of a sequence that is homologous to calponin. Calponin homology (CH) domains not only cross-link actin filaments into bundles and networks, but they also bind intermediate filaments and some signal transduction proteins to the actin cytoskeleton. This fundamental role of CH domains as a widely used actin-binding domain underlines the necessity to understand their structural interaction with actin. Using electron cryomicroscopy, we have determined the three-dimensional structure of F-actin and F-actin decorated with the NH2-terminal CH domains of fimbrin (N375). In a difference map between actin filaments and N375-decorated actin, one end of N375 is bound to a concave surface formed between actin subdomains 1 and 2 on two neighboring actin monomers. In addition, a fit of the atomic model for the actin filament to the maps reveals the actin residues that line, the binding surface. The binding of N375 changes actin, which we interpret as a movement of subdomain 1 away from the bound N375. This change in actin structure may affect its affinity for other actin-binding proteins and may be part of the regulation of the cytoskeleton itself. Difference maps between actin and actin decorated with other proteins provides a way to look for novel structural changes in actin.

scholarly journals Disruption of Primary Mesenchyme Cell Patterning by Misregulated Ectodermal Expression ofSpMsxin Sea Urchin Embryos

1998 ◽  
Vol 201 (2) ◽  
pp. 230-246 ◽  
Author(s):  
Hongying Tan ◽  
Andrew Ransick ◽  
Hailin Wu ◽  
Sonia Dobias ◽  
Yi-Hsin Liu ◽  
...  
Keyword(s):  
Sea Urchin ◽  
Cell Patterning ◽  
Sea Urchin Embryos ◽  
Mesenchyme Cell

scholarly journals Sulfate-Binding Protein (Sbp) from Xanthomonas citri: Structure and Functional Insights

2017 ◽  
Vol 30 (7) ◽  
pp. 578-588 ◽  
Author(s):  
Cristiane Tambascia Pereira ◽  
Cássia Roesler ◽  
Jéssica Nascimento Faria ◽  
Melissa Regina Fessel ◽  
Andrea Balan
Keyword(s):  
Abc Transporter ◽  
Structural Changes ◽  
Binding Protein ◽  
Functional Characterization ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Xanthomonas Citri ◽  
Canker Disease

The uptake and transport of sulfate in bacteria is mediated by an ATP-binding cassette transporter (ABC transporter) encoded by sbpcysUWA genes, whose importance has been widely demonstrated due to their relevance in cysteine synthesis and bacterial growth. In Xanthomonas citri, the causative agent of canker disease, the expression of components from this ABC transporter and others related to uptake of organic sulfur sources has been shown during in vitro growth cultures. In this work, based on gene reporter and proteomics analyses, we showed the activation of the promoter that controls the sbpcysUWA operon in vitro and in vivo and the expression of sulfate-binding protein (Sbp), a periplasmic-binding protein, indicating that this protein plays an important function during growth and that the transport system is active during Citrus sinensis infection. To characterize Sbp, we solved its three-dimensional structure bound to sulfate at 1.14 Å resolution and performed biochemical and functional characterization. The results revealed that Sbp interacts with sulfate without structural changes, but the interaction induces a significant increasing of protein thermal stability. Altogether, the results presented in this study show the evidence of the functionality of the ABC transporter for sulfate in X. citri and its relevance during infection.

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