scholarly journals Design and structural characterisation of olfactomedin-1 variants as tools for functional studies

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Matti F. Pronker ◽  
Hugo van den Hoek ◽  
Bert J. C. Janssen
Keyword(s):  
Binding Site ◽  
Calcium Binding ◽  
System Development ◽  
Nervous System Development ◽  
Mammalian Brain ◽  
Oligomeric State ◽  
Calcium Binding Site ◽  
X Ray ◽  
Structural Characterisation ◽  
Functional Studies

Abstract Background Olfactomedin-1 (Olfm1; also known as Noelin or Pancortin) is a highly-expressed secreted brain and retina protein and its four isoforms have different roles in nervous system development and function. Structural studies showed that the long Olfm1 isoform BMZ forms a disulfide-linked tetramer with a V-shaped architecture. The tips of the Olfm1 “V” each consist of two C-terminal β-propeller domains that enclose a calcium binding site. Functional characterisation of Olfm1 may be aided by new biochemical tools derived from these core structural elements. Results Here we present the production, purification and structural analysis of three novel monomeric, dimeric and tetrameric forms of mammalian Olfm1 for functional studies. We characterise these constructs structurally by high-resolution X-ray crystallography and small-angle X-ray scattering. The crystal structure of the Olfm1 β-propeller domain (to 1.25 Å) represents the highest-resolution structure of an olfactomedin family member to date, revealing features such as a hydrophilic tunnel containing water molecules running into the core of the domain where the calcium binding site resides. The shorter Olfactomedin-1 isoform BMY is a disulfide-linked tetramer with a shape similar to the corresponding region in the longer BMZ isoform. Conclusions These recombinantly-expressed protein tools should assist future studies, for example of biophysical, electrophysiological or morphological nature, to help elucidate the functions of Olfm1 in the mature mammalian brain. The control over the oligomeric state of Olfm1 provides a firm basis to better understand the role of Olfm1 in the (trans-synaptic) tethering or avidity-mediated clustering of synaptic receptors such as post-synaptic AMPA receptors and pre-synaptic amyloid precursor protein. In addition, the variation in domain composition of these protein tools provides a means to dissect the Olfm1 regions important for receptor binding.

scholarly journals Identification of the Calcium Binding Site and a Novel Ytterbium Site in Blood Coagulation Factor XIII by X-ray Crystallography

1999 ◽  
Vol 274 (8) ◽  
pp. 4917-4923 ◽  
Author(s):  
Brian A. Fox ◽  
Vivien C. Yee ◽  
Lars C. Pedersen ◽  
Isolde Le Trong ◽  
Paul D. Bishop ◽  
...  
Keyword(s):  
Binding Site ◽  
Blood Coagulation ◽  
Calcium Binding ◽  
Factor Xiii ◽  
Coagulation Factor ◽  
Calcium Binding Site ◽  
X Ray ◽  
X Ray Crystallography ◽  
Coagulation Factor Xiii

scholarly journals The X-ray structure of human calbindin-D28K: an improved model

2018 ◽  
Vol 74 (10) ◽  
pp. 1008-1014 ◽  
Author(s):  
James W. Noble ◽  
Rehab Almalki ◽  
S. Mark Roe ◽  
Armin Wagner ◽  
Ramona Duman ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Binding Site ◽  
Calcium Binding ◽  
Tertiary Structure ◽  
Nmr Structure ◽  
Calcium Binding Site ◽  
Globular Structure ◽  
Saxs Data ◽  
X Ray ◽  
Calbindin D28k

Calbindin-D28K is a widely expressed calcium-buffering cytoplasmic protein that is involved in many physiological processes. It has been shown to interact with other proteins, suggesting a role as a calcium sensor. Many of the targets of calbindin-D28K are of therapeutic interest: for example, inositol monophosphatase, the putative target of lithium therapy in bipolar disorder. Presented here is the first crystal structure of human calbindin-D28K. There are significant deviations in the tertiary structure when compared with the NMR structure of rat calbindin-D28K (PDB entry 2g9b), despite 98% sequence identity. Small-angle X-ray scattering (SAXS) indicates that the crystal structure better predicts the properties of calbindin-D28K in solution compared with the NMR structure. Here, the first direct visualization of the calcium-binding properties of calbindin-D28K is presented. Four of the six EF-hands that make up the secondary structure of the protein contain a calcium-binding site. Two distinct conformations of the N-terminal EF-hand calcium-binding site were identified using long-wavelength calcium single-wavelength anomalous dispersion (SAD). This flexible region has previously been recognized as a protein–protein interaction interface. SAXS data collected in both the presence and absence of calcium indicate that there are no large structural differences in the globular structure of calbindin-D28K between the calcium-loaded and unloaded proteins.

scholarly journals A disulfide bridge in the calcium binding site of a polyester hydrolase increases its thermal stability and activity against polyethylene terephthalate

FEBS Open Bio ◽  
2016 ◽  
Vol 6 (5) ◽  
pp. 425-432 ◽  
Author(s):  
Johannes Then ◽  
Ren Wei ◽  
Thorsten Oeser ◽  
André Gerdts ◽  
Juliane Schmidt ◽  
...  
Keyword(s):  
Thermal Stability ◽  
Binding Site ◽  
Polyethylene Terephthalate ◽  
Calcium Binding ◽  
Disulfide Bridge ◽  
Calcium Binding Site

scholarly journals Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila

2014 ◽  
Author(s):  
Sarah H Carl ◽  
Steven Russell
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Regulatory Networks ◽  
System Development ◽  
Nervous System Development ◽  
Phylogenetic Distance ◽  
Functional Sites ◽  
Sox Proteins ◽  
Alternative Sources ◽  
Group B

Background: Group B Sox proteins are a highly conserved group of transcription factors that act extensively to coordinate nervous system development in higher metazoans while showing both co-expression and functional redundancy across a broad group of taxa. In Drosophila melanogaster, the two group B Sox proteins Dichaete and SoxNeuro show widespread common binding across the genome. While some instances of functional compensation have been observed in Drosophila, the function of common binding and the extent of its evolutionary conservation is not known. Results: We used DamID-seq to examine the genome-wide binding patterns of Dichaete and SoxNeuro in four species of Drosophila. Through a quantitative comparison of Dichaete binding, we evaluated the rate of binding site turnover across the genome as well as at specific functional sites. We also examined the presence of Sox motifs within binding intervals and the correlation between sequence conservation and binding conservation. To determine whether common binding between Dichaete and SoxNeuro is conserved, we performed a detailed analysis of the binding patterns of both factors in two species. Conclusion: We find that, while the regulatory networks driven by Dichaete and SoxNeuro are largely conserved across the drosophilids studied, binding site turnover is widespread and correlated with phylogenetic distance. Nonetheless, binding is preferentially conserved at known cis-regulatory modules and core, independently verified binding sites. We observed the strongest binding conservation at sites that are commonly bound by Dichaete and SoxNeuro, suggesting that these sites are functionally important. Our analysis provides insights into the evolution of group B Sox function, highlighting the specific conservation of shared binding sites and suggesting alternative sources of neofunctionalisation between paralogous family members.

Calcium-Binding Site β2, Adjacent to the “b” Polymerization Site, Modulates Lateral Aggregation of Protofibrils during Fibrin Polymerization†,‡

Biochemistry ◽  
2004 ◽  
Vol 43 (9) ◽  
pp. 2475-2483 ◽  
Author(s):  
Michael S. Kostelansky ◽  
Karim C. Lounes ◽  
Li Fang Ping ◽  
Sarah K. Dickerson ◽  
Oleg V. Gorkun ◽  
...  
Keyword(s):  
Binding Site ◽  
Calcium Binding ◽  
Calcium Binding Site ◽  
Fibrin Polymerization
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