scholarly journals Carbohydrate-binding modules influence substrate specificity of an endoglucanase from Clostridium thermocellum

2015 ◽  
Vol 80 (1) ◽  
pp. 188-192 ◽  
Author(s):  
Shunsuke Ichikawa ◽  
Mitsuki Yoshida ◽  
Shuichi Karita ◽  
Makoto Kondo ◽  
Masakazu Goto
Keyword(s):  
Substrate Specificity ◽  
Clostridium Thermocellum ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Modules

scholarly journals The family 6 carbohydrate-binding modules have coevolved with their appended catalytic modules toward similar substrate specificity

Glycobiology ◽  
2009 ◽  
Vol 19 (6) ◽  
pp. 615-623 ◽  
Author(s):  
Gurvan Michel ◽  
Tristan Barbeyron ◽  
Bernard Kloareg ◽  
Mirjam Czjzek
Keyword(s):  
Substrate Specificity ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Modules ◽  
The Family

Solution structure, dynamics and binding studies of a family 11 carbohydrate-binding module from Clostridium thermocellum (CtCBM11)

2013 ◽  
Vol 451 (2) ◽  
pp. 289-300 ◽  
Author(s):  
Aldino Viegas ◽  
João Sardinha ◽  
Filipe Freire ◽  
Daniel F. Duarte ◽  
Ana L. Carvalho ◽  
...  
Keyword(s):  
Clostridium Thermocellum ◽  
Solution Structure ◽  
Close Contact ◽  
Van Der Waals Interactions ◽  
Backbone Dynamics ◽  
Titration Calorimetry ◽  
Carbohydrate Binding ◽  
Binding Studies ◽  
Carbohydrate Binding Modules ◽  
Wide Range

Non-catalytic cellulosomal CBMs (carbohydrate-binding modules) are responsible for increasing the catalytic efficiency of cellulosic enzymes by selectively putting the substrate (a wide range of poly- and oligo-saccharides) and enzyme into close contact. In the present study we carried out an atomistic rationalization of the molecular determinants of ligand specificity for a family 11 CBM from thermophilic Clostridium thermocellum [CtCBM11 (C. thermocellum CBM11)], based on a NMR and molecular modelling approach. We have determined the NMR solution structure of CtCBM11 at 25°C and 50°C and derived information on the residues of the protein that are involved in ligand recognition and on the influence of the length of the saccharide chain on binding. We obtained models of the CtCBM11–cellohexaose and CtCBM11–cellotetraose complexes by docking in accordance with the NMR experimental data. Specific ligand–protein CH-π and Van der Waals interactions were found to be determinant for the stability of the complexes and for defining specificity. Using the order parameters derived from backbone dynamics analysis in the presence and absence of ligand and at 25°C and 50°C, we determined that the protein's backbone conformational entropy is slightly positive. This data in combination with the negative binding entropy calculated from ITC (isothermal titration calorimetry) studies supports a selection mechanism where a rigid protein selects a defined oligosaccharide conformation.

Properties of four C-terminal carbohydrate-binding modules (CBM4) of laminarinase Lic16A of Clostridium thermocellum

2012 ◽  
Vol 46 (6) ◽  
pp. 817-822 ◽  
Author(s):  
I. A. Dvortsov ◽  
N. A. Lunina ◽  
V. V. Zverlov ◽  
G. A. Velikodvorskaya
Keyword(s):  
Clostridium Thermocellum ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Modules

scholarly journals Functional diversity of three tandem C-terminal carbohydrate-binding modules of a β-mannanase

2021 ◽  
pp. 100638
Author(s):  
Marie Sofie Møller ◽  
Souad El Bouaballati ◽  
Bernard Henrissat ◽  
Birte Svensson
Keyword(s):  
Functional Diversity ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Modules

scholarly journals Functionalization of Cellulose-Based Hydrogels with Bi-Functional Fusion Proteins Containing Carbohydrate-Binding Modules

Materials ◽  
2021 ◽  
Vol 14 (12) ◽  
pp. 3175
Author(s):  
Mariana Barbosa ◽  
Hélvio Simões ◽  
Duarte Miguel F. Prazeres
Keyword(s):  
Fusion Proteins ◽  
Fluorescent Protein ◽  
Protein A ◽  
Chemical Properties ◽  
Main Idea ◽  
Bioactive Molecules ◽  
Scaffolding Protein ◽  
Carbohydrate Binding ◽  
Biological Interactions ◽  
Carbohydrate Binding Modules

Materials with novel and enhanced functionalities can be obtained by modifying cellulose with a range of biomolecules. This functionalization can deliver tailored cellulose-based materials with enhanced physical and chemical properties and control of biological interactions that match specific applications. One of the foundations for the success of such biomaterials is to efficiently control the capacity to combine relevant biomolecules into cellulose materials in such a way that the desired functionality is attained. In this context, our main goal was to develop bi-functional biomolecular constructs for the precise modification of cellulose hydrogels with bioactive molecules of interest. The main idea was to use biomolecular engineering techniques to generate and purify different recombinant fusions of carbohydrate binding modules (CBMs) with significant biological entities. Specifically, CBM-based fusions were designed to enable the bridging of proteins or oligonucleotides with cellulose hydrogels. The work focused on constructs that combine a family 3 CBM derived from the cellulosomal-scaffolding protein A from Clostridium thermocellum (CBM3) with the following: (i) an N-terminal green fluorescent protein (GFP) domain (GFP-CBM3); (ii) a double Z domain that recognizes IgG antibodies; and (iii) a C-terminal cysteine (CBM3C). The ability of the CBM fusions to bind and/or anchor their counterparts onto the surface of cellulose hydrogels was evaluated with pull-down assays. Capture of GFP-CBM3 by cellulose was first demonstrated qualitatively by fluorescence microscopy. The binding of the fusion proteins, the capture of antibodies (by ZZ-CBM3), and the grafting of an oligonucleotide (to CBM3C) were successfully demonstrated. The bioactive cellulose platform described here enables the precise anchoring of different biomolecules onto cellulose hydrogels and could contribute significatively to the development of advanced medical diagnostic sensors or specialized biomaterials, among others.

scholarly journals Integrated Counts of Carbohydrate-Active Protein Domains as Metabolic Readouts to Distinguish Probiotic Biology and Human Fecal Metagenomes

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Hong-Hsing Liu ◽  
Yu-Chen Lin ◽  
Chen-Shuan Chung ◽  
Kevin Liu ◽  
Ya-Hui Chang ◽  
...  
Keyword(s):  
Markov Models ◽  
Protein Domains ◽  
Degradation Pathway ◽  
The Other ◽  
Carbohydrate Binding ◽  
Gram Stain ◽  
Active Protein ◽  
Metabolic Potential ◽  
Independent Validation ◽  
Carbohydrate Binding Modules

AbstractBowel microbiota is a “metaorgan” of metabolisms on which quantitative readouts must be performed before interventions can be introduced and evaluated. The study of the effects of probiotic Clostridium butyricum MIYAIRI 588 (CBM588) on intestine transplantees indicated an increased percentage of the “other glycan degradation” pathway in 16S-rRNA-inferred metagenomes. To verify the prediction, a scoring system of carbohydrate metabolisms derived from shotgun metagenomes was developed using hidden Markov models. A significant correlation (R = 0.9, p < 0.015) between both modalities was demonstrated. An independent validation revealed a strong complementarity (R = −0.97, p < 0.002) between the scores and the abundance of “glycogen degradation” in bacteria communities. On applying the system to bacteria genomes, CBM588 had only 1 match and ranked higher than the other 8 bacteria evaluated. The gram-stain properties were significantly correlated to the scores (p < 5 × 10−4). The distributions of the scored protein domains indicated that CBM588 had a considerably higher (p < 10−5) proportion of carbohydrate-binding modules than other bacteria, which suggested the superior ability of CBM588 to access carbohydrates as a metabolic driver to the bowel microbiome. These results demonstrated the use of integrated counts of protein domains as a feasible readout for metabolic potential within bacteria genomes and human metagenomes.

scholarly journals Family 6 carbohydrate-binding modules display multiple β1,3-linked glucan-specific binding interfaces

2009 ◽  
Vol 300 (1) ◽  
pp. 48-57 ◽  
Author(s):  
Márcia A.S. Correia ◽  
Virgínia M.R. Pires ◽  
Harry J. Gilbert ◽  
David N. Bolam ◽  
Vânia O. Fernandes ◽  
...  
Keyword(s):  
Specific Binding ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Modules ◽  
Binding Interfaces

scholarly journals Versatile derivatives of carbohydrate-binding modules for imaging of complex carbohydrates approaching the molecular level of resolution

BioTechniques ◽  
2006 ◽  
Vol 41 (4) ◽  
pp. 435-443 ◽  
Author(s):  
Shi-You Ding ◽  
Qi Xu ◽  
Mursheda K. Ali ◽  
John O. Baker ◽  
Edward A. Bayer ◽  
...  
Keyword(s):  
Molecular Level ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Modules ◽  
Complex Carbohydrates ◽  
Derivatives Of

Novel clostridial cell-surface hemicellulose-binding CBM3 proteins

2021 ◽  
Vol 77 (4) ◽  
Author(s):  
Almog Hershko Rimon ◽  
Oded Livnah ◽  
Inna Rozman Grinberg ◽  
Lizett Ortiz de Ora ◽  
Oren Yaniv ◽  
...  
Keyword(s):  
Calcium Binding ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Carbohydrate Binding ◽  
Unexpected Finding ◽  
Calcium Binding Site ◽  
Three Dimensional Structure ◽  
Loop Region ◽  
Carbohydrate Binding Modules ◽  
Cellulose Binding

A novel member of the family 3 carbohydrate-binding modules (CBM3s) is encoded by a gene (Cthe_0271) in Clostridium thermocellum which is the most highly expressed gene in the bacterium during its growth on several types of biomass substrates. Surprisingly, CtCBM3-0271 binds to at least two different types of xylan, instead of the common binding of CBM3s to cellulosic substrates. CtCBM3-0271 was crystallized and its three-dimensional structure was solved and refined to a resolution of 1.8 Å. In order to learn more about the role of this type of CBM3, a comparative study with its orthologue from Clostridium clariflavum (encoded by the Clocl_1192 gene) was performed, and the three-dimensional structure of CcCBM3-1192 was determined to 1.6 Å resolution. Carbohydrate binding by CcCBM3-1192 was found to be similar to that by CtCBM3-0271; both exhibited binding to xylan rather than to cellulose. Comparative structural analysis of the two CBM3s provided a clear functional correlation of structure and binding, in which the two CBM3s lack the required number of binding residues in their cellulose-binding strips and thus lack cellulose-binding capabilities. This is an enigma, as CtCBM3-0271 was reported to be a highly expressed protein when the bacterium was grown on cellulose. An additional unexpected finding was that CcCBM3-1192 does not contain the calcium ion that was considered to play a structural stabilizing role in the CBM3 family. Despite the lack of calcium, the five residues that form the calcium-binding site are conserved. The absence of calcium results in conformational changes in two loops of the CcCBM3-1192 structure. In this context, superposition of the non-calcium-binding CcCBM3-1192 with CtCBM3-0271 and other calcium-binding CBM3s reveals a much broader two-loop region in the former compared with CtCBM3-0271.

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