scholarly journals Structure of a consensus chitin-binding domain revealed by solution NMR

2020 ◽  
Author(s):  
Dario Heymann ◽  
Harini Mohanram ◽  
Akshita Kumar ◽  
Chandra S. Verma ◽  
Julien Lescar ◽  
...  
Keyword(s):  
Binding Proteins ◽  
3D Structure ◽  
Binding Domain ◽  
Biomimetic Synthesis ◽  
Binding Motif ◽  
Carbohydrate Binding ◽  
Dosidicus Gigas ◽  
Chitin Binding Domain ◽  
Carbohydrate Degradation ◽  
Wide Range

ABSTRACTCarbohydrate-binding proteins (CBPs) are a versatile group of proteins found in almost every organism on earth. CBPs are involved in enzymatic carbohydrate degradation and also serve as templating scaffolds in the exoskeleton of crustaceans and insects. One specific chitin-binding motif found across a wide range of arthropods’ exoskeletons is the “extended Rebers and Riddiford” consensus (R&R). However, how the R&R motif binds chitin is unclear. Here, we report the 3D structure and molecular level interactions of a chitin-binding domain (CBD-γ) located in a CBP from the beak of the jumbo squid Dosidicus gigas. This CBP is one of four chitin-binding proteins identified in the beak mouthpart of D. gigas and is believed to interact with chitin to form a scaffold network that is infiltrated with a second set of structural proteins during beak maturation. We used solution state NMR spectroscopy to elucidate the molecular interactions between CBD-γ and the soluble chitin derivative pentaacetyl-chitopentaose (PCP) and find that folding of this domain is triggered upon its interaction with PCP. To our knowledge, this is the first experimental 3D structure of a CBP containing the R&R consensus motif, which can be used as a template to understand in more details the role of the R&R motif found in a wide range of CBP-chitin complexes. The present structure also provides molecular information for biomimetic synthesis of graded biomaterials using aqueous-based chemistry and biopolymers.

scholarly journals Immobilization of Cells with Surface-Displayed Chitin-Binding Domain

2006 ◽  
Vol 72 (1) ◽  
pp. 927-931 ◽  
Author(s):  
Jen-You Wang ◽  
Yun-Peng Chao
Keyword(s):  
Escherichia Coli ◽  
Gene Fusion ◽  
Cell Immobilization ◽  
Binding Domain ◽  
Engineering Applications ◽  
Chitin Binding Domain ◽  
Wide Range ◽  
Frame Fusion

ABSTRACT To explore chitin-binding domain (ChBD)-based cell immobilization, a tripartite gene fusion consisting of an in-frame fusion of ChBD to lpp and ompA was constructed and expressed in Escherichia coli. ChBD-displayed cells exhibited highly specific and stable binding to chitin within a wide range of pHs (5 to 8) and temperatures (15 to 37°C). These results illustrate the promising use of this approach for engineering applications.

scholarly journals Expression and Characterization of the Chitin-Binding Domain of Chitinase A1 from Bacillus circulans WL-12

2000 ◽  
Vol 182 (11) ◽  
pp. 3045-3054 ◽  
Author(s):  
Masayuki Hashimoto ◽  
Takahisa Ikegami ◽  
Shizuka Seino ◽  
Nobuhumi Ohuchi ◽  
Harumi Fukada ◽  
...  
Keyword(s):  
Hydrophobic Interactions ◽  
Expression System ◽  
Binding Activity ◽  
Binding Domain ◽  
Bacillus Circulans ◽  
Titration Calorimetry ◽  
Affinity Column ◽  
Chitin Binding Domain ◽  
Wide Range ◽  
Hydrolysis Of

ABSTRACT Chitinase A1 from Bacillus circulans WL-12 comprises an N-terminal catalytic domain, two fibronectin type III-like domains, and a C-terminal chitin-binding domain (ChBD). In order to study the biochemical properties and structure of the ChBD, ChBDChiA1 was produced in Escherichia coliusing a pET expression system and purified by chitin affinity column chromatography. Purified ChBDChiA1 specifically bound to various forms of insoluble chitin but not to other polysaccharides, including chitosan, cellulose, and starch. Interaction of soluble chitinous substrates with ChBDChiA1 was not detected by means of nuclear magnetic resonance and isothermal titration calorimetry. In addition, the presence of soluble substrates did not interfere with the binding of ChBDChiA1 to regenerated chitin. These observations suggest that ChBDChiA1recognizes a structure which is present in insoluble or crystalline chitin but not in chito-oligosaccharides or in soluble derivatives of chitin. ChBDChiA1 exhibited binding activity over a wide range of pHs, and the binding activity was enhanced at pHs near its pI and by the presence of NaCl, suggesting that the binding of ChBDChiA1 is mediated mainly by hydrophobic interactions. Hydrolysis of β-chitin microcrystals by intact chitinase A1 and by a deletion derivative lacking the ChBD suggested that the ChBD is not absolutely required for hydrolysis of β-chitin microcrystals but greatly enhances the efficiency of degradation.

Carbohydrate Binding Specificity of the Recombinant Chitin-binding Domain of Human Macrophage Chitinase

2003 ◽  
Vol 67 (11) ◽  
pp. 2402-2407 ◽  
Author(s):  
Minoru UJITA ◽  
Kaori SAKAI ◽  
Keishi HAMAZAKI ◽  
Masahiko YONEDA ◽  
Shigeki ISOMURA ◽  
...  
Keyword(s):  
Binding Specificity ◽  
Binding Domain ◽  
Human Macrophage ◽  
Carbohydrate Binding ◽  
Chitin Binding Domain

Molecular Characterization of Rotavirus Porcine OSU Carbohydrate- Binding Domain VP8*

2015 ◽  
Vol 12 (1) ◽  
pp. 69-72
Author(s):  
Hao Li ◽  
Wei Zhang ◽  
Hong-hao Zhou ◽  
Xiao-li Li
Keyword(s):  
Molecular Characterization ◽  
Binding Domain ◽  
Carbohydrate Binding

scholarly journals A Fungal Defensin Targets the SARS−CoV−2 Spike Receptor−Binding Domain

2021 ◽  
Vol 7 (7) ◽  
pp. 553
Author(s):  
Bin Gao ◽  
Shunyi Zhu
Keyword(s):  
Receptor Binding ◽  
Viral Entry ◽  
Single Point ◽  
Binding Domain ◽  
Host Cells ◽  
Single Point Mutation ◽  
Binding Motif ◽  
Microsporum Canis ◽  
Receptor Binding Domain ◽  
Fungal Defensin

Coronavirus Disease 2019 (COVID−19) elicited by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS−CoV−2) is calling for novel targeted drugs. Since the viral entry into host cells depends on specific interactions between the receptor−binding domain (RBD) of the viral Spike protein and the membrane−bound monocarboxypeptidase angiotensin converting enzyme 2 (ACE2), the development of high affinity RBD binders to compete with human ACE2 represents a promising strategy for the design of therapeutics to prevent viral entry. Here, we report the discovery of such a binder and its improvement via a combination of computational and experimental approaches. The binder micasin, a known fungal defensin from the dermatophytic fungus Microsporum canis with antibacterial activity, can dock to the crevice formed by the receptor−binding motif (RBM) of RBD via an extensive shape complementarity interface (855.9 Å2 in area) with numerous hydrophobic and hydrogen−bonding interactions. Using microscale thermophoresis (MST) technique, we confirmed that micasin and its C−terminal γ−core derivative with multiple predicted interacting residues exhibited a low micromolar affinity to RBD. Expanding the interface area of micasin through a single point mutation to 970.5 Å2 accompanying an enhanced hydrogen bond network significantly improved its binding affinity by six−fold. Our work highlights the naturally occurring fungal defensins as an emerging resource that may be suitable for the development into antiviral agents for COVID−19.

scholarly journals Chemical Synthesis and NMR Solution Structure of Conotoxin GXIA from Conus geographus

Marine Drugs ◽  
2021 ◽  
Vol 19 (2) ◽  
pp. 60
Author(s):  
David A. Armstrong ◽  
Ai-Hua Jin ◽  
Nayara Braga Emidio ◽  
Richard J. Lewis ◽  
Paul F. Alewood ◽  
...  
Keyword(s):  
Solution Structure ◽  
3D Structure ◽  
Voltage Sensor ◽  
Solution Nmr ◽  
Striking Similarity ◽  
Amino Acid Peptide ◽  
Wide Range ◽  
Cone Snails ◽  
Drug Leads ◽  
Β Sheet

Conotoxins are disulfide-rich peptides found in the venom of cone snails. Due to their exquisite potency and high selectivity for a wide range of voltage and ligand gated ion channels they are attractive drug leads in neuropharmacology. Recently, cone snails were found to have the capability to rapidly switch between venom types with different proteome profiles in response to predatory or defensive stimuli. A novel conotoxin, GXIA (original name G117), belonging to the I3-subfamily was identified as the major component of the predatory venom of piscivorous Conus geographus. Using 2D solution NMR spectroscopy techniques, we resolved the 3D structure for GXIA, the first structure reported for the I3-subfamily and framework XI family. The 32 amino acid peptide is comprised of eight cysteine residues with the resultant disulfide connectivity forming an ICK+1 motif. With a triple stranded β-sheet, the GXIA backbone shows striking similarity to several tarantula toxins targeting the voltage sensor of voltage gated potassium and sodium channels. Supported by an amphipathic surface, the structural evidence suggests that GXIA is able to embed in the membrane and bind to the voltage sensor domain of a putative ion channel target.

scholarly journals Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Alice Massacci ◽  
Eleonora Sperandio ◽  
Lorenzo D’Ambrosio ◽  
Mariano Maffei ◽  
Fabio Palombo ◽  
...  
Keyword(s):  
Receptor Binding ◽  
Consensus Sequence ◽  
Cell Epitope ◽  
Vaccine Design ◽  
Binding Domain ◽  
Spike Protein ◽  
Antibody Activity ◽  
Binding Motif ◽  
Receptor Binding Domain ◽  
The Impact

Abstract Background Tracking the genetic variability of Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) is a crucial challenge. Mainly to identify target sequences in order to generate robust vaccines and neutralizing monoclonal antibodies, but also to track viral genetic temporal and geographic evolution and to mine for variants associated with reduced or increased disease severity. Several online tools and bioinformatic phylogenetic analyses have been released, but the main interest lies in the Spike protein, which is the pivotal element of current vaccine design, and in the Receptor Binding Domain, that accounts for most of the neutralizing the antibody activity. Methods Here, we present an open-source bioinformatic protocol, and a web portal focused on SARS-CoV-2 single mutations and minimal consensus sequence building as a companion vaccine design tool. Furthermore, we provide immunogenomic analyses to understand the impact of the most frequent RBD variations. Results Results on the whole GISAID sequence dataset at the time of the writing (October 2020) reveals an emerging mutation, S477N, located on the central part of the Spike protein Receptor Binding Domain, the Receptor Binding Motif. Immunogenomic analyses revealed some variation in mutated epitope MHC compatibility, T-cell recognition, and B-cell epitope probability for most frequent human HLAs. Conclusions This work provides a framework able to track down SARS-CoV-2 genomic variability.

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