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Rooijakkers BJM, Arola S, Velagapudi R, Linder MB. Different effects of carbohydrate binding modules on the viscoelasticity of nanocellulose gels. Biochem Biophys Rep 2020; 22:100766. [PMID: 32337376 PMCID: PMC7176825 DOI: 10.1016/j.bbrep.2020.100766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/19/2020] [Accepted: 04/07/2020] [Indexed: 12/11/2022] Open
Abstract
Many cellulose degrading and modifying enzymes have distinct parts called carbohydrate binding modules (CBMs). The CBMs have been shown to increase the concentration of enzymes on the insoluble substrate and thereby enhance catalytic activity. It has been suggested that CBMs also have a role in disrupting or dispersing the insoluble cellulose substrate, but dispute remains and explicit evidence of such a mechanism is lacking. We produced the isolated CBMs from two major cellulases (Cel6A and Cel7A) from Trichoderma reesei as recombinant proteins in Escherichia coli. We then studied the viscoelastic properties of native unmodified cellulose nanofibrils (CNF) in combination with the highly purified CBMs to detect possible functional effects of the CBMs on the CNF. The two CBMs showed clearly different effects on the viscoelastic properties of CNF. The difference in effects is noteworthy, yet it was not possible to conclude for example disruptive effects. We discuss here the alternative explanations for viscoelastic effects on CNF caused by CBMs, including the effect of ionic cosolutes. The effect of Cellulose Binding Modules (CBM) on the viscoelastic properties of cellulose nanofibers (CNF) were investigated. The CBMs from enzymes Cel6A and Cel7A from Trichoderma reesei affected the rheology of CNF very differently. Additions of even very small amounts of salt (NaCl) also affected the rheology of CNF. The high sensitivity of NFC towards added ionic species makes interpretation of results challenging.
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Affiliation(s)
- Bart J M Rooijakkers
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, 02150, Espoo, Finland
| | - Suvi Arola
- VTT, Technical Research Centre of Finland Ltd., High Performance Fiber Products, Tietotie 4E, 02150, Espoo, Finland
| | - Rama Velagapudi
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, 02150, Espoo, Finland
| | - Markus B Linder
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, 02150, Espoo, Finland
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2
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Positive surface charge of GluN1 N-terminus mediates the direct interaction with EphB2 and NMDAR mobility. Nat Commun 2020; 11:570. [PMID: 31996679 PMCID: PMC6989673 DOI: 10.1038/s41467-020-14345-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 12/19/2019] [Indexed: 12/31/2022] Open
Abstract
Localization of the N-methyl-D-aspartate type glutamate receptor (NMDAR) to dendritic spines is essential for excitatory synaptic transmission and plasticity. Rather than remaining trapped at synaptic sites, NMDA receptors undergo constant cycling into and out of the postsynaptic density. Receptor movement is constrained by protein-protein interactions with both the intracellular and extracellular domains of the NMDAR. The role of extracellular interactions on the mobility of the NMDAR is poorly understood. Here we demonstrate that the positive surface charge of the hinge region of the N-terminal domain in the GluN1 subunit of the NMDAR is required to maintain NMDARs at dendritic spine synapses and mediates the direct extracellular interaction with a negatively charged phospho-tyrosine on the receptor tyrosine kinase EphB2. Loss of the EphB-NMDAR interaction by either mutating GluN1 or knocking down endogenous EphB2 increases NMDAR mobility. These findings begin to define a mechanism for extracellular interactions mediated by charged domains.
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3
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Watanabe H, Yoshida C, Ooishi A, Nakai Y, Ueda M, Isobe Y, Honda S. Histidine-Mediated Intramolecular Electrostatic Repulsion for Controlling pH-Dependent Protein-Protein Interaction. ACS Chem Biol 2019; 14:2729-2736. [PMID: 31596562 DOI: 10.1021/acschembio.9b00652] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein-protein interactions that can be controlled by environmental triggers have immense potential in various biological and industrial applications. In the current study, we aimed to engineer a pH-dependent protein-protein interaction that employs intramolecular electrostatic repulsion through a structure-guided histidine substitution approach. We implemented this strategy on Streptococcal protein G, an affinity ligand for immunoglobulin G, and showed that even a single point mutation effectively improved the pH sensitivity of the binding interactions without adversely affecting its structural stability or its innate binding function. Depending on the pH of the environment, the protein-protein interaction was disrupted by the electrostatic repulsion between the substituted histidine and its neighboring positively charged residues. Structurally, the substituted histidine residue was located adjacent to a lysine residue that could form hydrogen bonds with immunoglobulin G. Thermodynamically, the introduced electrostatic repulsion was reflected in the significant loss of the exothermic heat of the binding under acidic conditions, whereas accompanying enthalpy-entropy compensation partly suppressed the improvement of the pH sensitivity. Thus, the engineered pH-sensitive protein G could enable antibody purification under mildly acidic conditions. This intramolecular design can be combined with conventional protein-protein interface design. Moreover, the method proposed here provides us with additional design criteria for optimization of pH-dependent molecular interactions.
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Affiliation(s)
- Hideki Watanabe
- The National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba 305-8566, Japan
| | - Chuya Yoshida
- The National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba 305-8566, Japan
| | - Ayako Ooishi
- The National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba 305-8566, Japan
| | - Yasuto Nakai
- Daicel Corporation, Innovation Park, 1239, Shinzaike, Aboshi, Himeji, Hyogo 671-1283, Japan
| | - Momoko Ueda
- Daicel Corporation, Innovation Park, 1239, Shinzaike, Aboshi, Himeji, Hyogo 671-1283, Japan
| | - Yutaka Isobe
- Daicel Corporation, Innovation Park, 1239, Shinzaike, Aboshi, Himeji, Hyogo 671-1283, Japan
| | - Shinya Honda
- The National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba 305-8566, Japan
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4
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Voutilainen S, Paananen A, Lille M, Linder MB. Modular protein architectures for pH-dependent interactions and switchable assembly of nanocellulose. Int J Biol Macromol 2019; 137:270-276. [PMID: 31260762 DOI: 10.1016/j.ijbiomac.2019.06.227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/17/2019] [Accepted: 06/28/2019] [Indexed: 11/27/2022]
Abstract
Protein engineering shows a wide range of possibilities for designing properties in novel materials. Following inspiration from natural systems we have studied how combinations or duplications of protein modules can be used to engineer their interactions and achieve functional properties. Here we used cellulose binding modules (CBM) coupled to spider silk N-terminal domains that dimerize in a pH-sensitive manner. We showed how the pH-sensitive switching into dimers affected cellulose binding affinity in relation to covalent coupling between CBMs. Finally, we showed how the pH-sensitive coupling could be used to assemble cellulose nanofibers in a dynamic pH-dependent way. The work shows how novel proteins can be designed by linking functional domains from widely different sources and thereby achieve new functions in the self-assembly of nanoscale materials.
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Affiliation(s)
- Sanni Voutilainen
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Box 16100, 00076, Aalto, Espoo, Finland; VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044 VTT Espoo, Finland
| | - Arja Paananen
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044 VTT Espoo, Finland
| | - Martina Lille
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044 VTT Espoo, Finland
| | - Markus B Linder
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Box 16100, 00076, Aalto, Espoo, Finland.
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5
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Fungal-type carbohydrate binding modules from the coccolithophore Emiliania huxleyi show binding affinity to cellulose and chitin. PLoS One 2018; 13:e0197875. [PMID: 29782536 PMCID: PMC5962083 DOI: 10.1371/journal.pone.0197875] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/09/2018] [Indexed: 12/21/2022] Open
Abstract
Six fungal-type cellulose binding domains were found in the genome of the coccolithophore Emiliania huxleyi and cloned and expressed in Escherichia coli. Sequence comparison indicate high similarity to fungal cellulose binding domains, raising the question of why these domains exist in coccolithophores. The proteins were tested for binding with cellulose and chitin as ligands, which resulted in the identification of two functional carbohydrate binding modules: EHUX2 and EHUX4. Compared to benchmark fungal cellulose binding domain Cel7A-CBM1 from Trichoderma reesei, these proteins showed slightly lower binding to birch and bacterial cellulose, but were more efficient chitin binders. Finally, a set of cellulose binding domains was created based on the shuffling of one well-functioning and one non-functional domain. These were characterized in order to get more information of the binding domain’s sequence–function relationship, indicating characteristic differences between the molecular basis of cellulose versus chitin recognition. As previous reports have showed the presence of cellulose in coccoliths and here we find functional cellulose binding modules, a possible connection is discussed.
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Happs RM, Guan X, Resch MG, Davis MF, Beckham GT, Tan Z, Crowley MF. O-glycosylation effects on family 1 carbohydrate-binding module solution structures. FEBS J 2015; 282:4341-56. [PMID: 26307003 DOI: 10.1111/febs.13500] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 08/18/2015] [Accepted: 08/21/2015] [Indexed: 01/20/2023]
Abstract
UNLABELLED Family 1 carbohydrate-binding modules (CBMs) are ubiquitous components of multimodular fungal enzymes that degrade plant cell wall polysaccharides and bind specifically to cellulose. Native glycosylation of family 1 CBMs has been shown to substantially impact multiple physical properties, including thermal and proteolytic stability and cellulose binding affinity. To gain molecular insights into the changes in CBM properties upon glycosylation, solution structures of two glycoforms of a Trichoderma reesei family 1 CBM were studied by NMR spectroscopy: a glycosylated family 1 CBM with a mannose group attached to both Thr1 and Ser3 and a second family 1 CBM with single mannose groups attached to Thr1, Ser3 and Ser14. The structures clearly reveal that monosaccharides at both Ser3 and Ser14 on family 1 CBMs present additional cellulose binding platforms, similar to well-characterized aromatic residues at the binding interface, which align to the cellulose surface. These results are in agreement with previous experimental work demonstrating that glycans at Ser3 and Ser14 impart significant improvements in binding affinity. Additionally, detailed analysis of the NMR structures and molecular simulations indicates that the protein backbone of the CBM is not significantly altered by attachment of monosaccharides, and that the mannose attached to Ser14 may be more flexible than the mannose at Ser3. Overall, the present study reveals how family 1 CBM structures are affected by covalent attachment of monosaccharides, which are likely important post-translational modifications of these common subdomains of fungal plant cell wall degrading enzymes. DATABASE Structural data have been deposited in the RCSB Protein Data Bank (PDB codes: 2MWJ and 2MWK) and the BioMagRes Bank (BMRB codes: 25331 and 25332) for CBM_M2 and CBM_M3, respectively.
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Affiliation(s)
- Renee M Happs
- National Renewable Energy Laboratory, National Bioenergy Center, Golden, CO, USA
| | - Xiaoyang Guan
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Michael G Resch
- National Renewable Energy Laboratory, National Bioenergy Center, Golden, CO, USA
| | - Mark F Davis
- National Renewable Energy Laboratory, National Bioenergy Center, Golden, CO, USA
| | - Gregg T Beckham
- National Renewable Energy Laboratory, National Bioenergy Center, Golden, CO, USA
| | - Zhongping Tan
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Michael F Crowley
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, USA
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7
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Payne CM, Knott BC, Mayes HB, Hansson H, Himmel ME, Sandgren M, Ståhlberg J, Beckham GT. Fungal Cellulases. Chem Rev 2015; 115:1308-448. [DOI: 10.1021/cr500351c] [Citation(s) in RCA: 533] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christina M. Payne
- Department
of Chemical and Materials Engineering and Center for Computational
Sciences, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, Kentucky 40506, United States
| | - Brandon C. Knott
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Heather B. Mayes
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Henrik Hansson
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Michael E. Himmel
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Mats Sandgren
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Jerry Ståhlberg
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Gregg T. Beckham
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
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8
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Tang B, Zhang Y, Yang Y, Song Z, Li X. Expression and functional analysis of a glycoside hydrolase family 45 endoglucanase from Rhizopus stolonifer. World J Microbiol Biotechnol 2014; 30:2943-52. [PMID: 25164957 DOI: 10.1007/s11274-014-1722-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Accepted: 08/11/2014] [Indexed: 11/29/2022]
Abstract
A novel endoglucanase gene was cloned from Rhizopus stolonifer and expressed in Escherichia coli, the gene product EG II (45 kDa) was assigned to Glycoside Hydrolase Family 45 (GH45), and its specific activity on phosphoric acid-swollen cellulose (PASC) was 48 IU/mg. To solve the problem of substrate accumulation in the cellulose hydrolysis and enhance the catalytic efficiency of endoglucanase, the eg2 gene was modified by site directed mutagenesis. Mutations generated by overlapping PCR have been proven to increase its catalytic activity on carboxymenthyl cellulose, microcrystalline cellulose (Avicel) and PASC, among which the mutant EG II-E containing all 6 mutations (N39S, V136D, T251G, D255G, P256S and E260D) peaked 121 IU/mg on PASC. The bioinformatic analysis showed that 2 key catalytic residues (D136 and D260) moved closer with the opening of a loop after mutagenesis, and a tunnel was formed by structural transformation. This structure was conducive for the substrate to access the active centre, and D136 played an indispensable role in the substrate recognition.
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Affiliation(s)
- Bin Tang
- College of Biochemical Engineering, Anhui Polytechnic University, Wuhu, 241000, China,
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9
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Tsukamoto M, Watanabe H, Ooishi A, Honda S. Engineered protein A ligands, derived from a histidine-scanning library, facilitate the affinity purification of IgG under mild acidic conditions. J Biol Eng 2014; 8:15. [PMID: 25057290 PMCID: PMC4107488 DOI: 10.1186/1754-1611-8-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Accepted: 06/21/2014] [Indexed: 11/18/2022] Open
Abstract
Background In antibody purification processes, the acidic buffer commonly used to elute the bound antibodies during conventional affinity chromatograph, can damage the antibody. Herein we describe the development of several types of affinity ligands which enable the purification of antibodies under much milder conditions. Results Staphylococcal protein A variants were engineered by using both structure-based design and combinatorial screening methods. The frequency of amino acid residue substitutions was statistically analyzed using the sequences isolated from a histidine-scanning library screening. The positions where the frequency of occurrence of a histidine residue was more than 70% were thought to be effective histidine-mutation sites. Consequently, we identified PAB variants with a D36H mutation whose binding of IgG was highly sensitive to pH change. Conclusion The affinity column elution chromatograms demonstrated that antibodies could be eluted at a higher pH (∆pH**≧2.0) than ever reported (∆pH = 1.4) when the Staphylococcal protein A variants developed in this study were used as affinity ligands. The interactions between Staphylococcal protein A and IgG-Fab were shown to be important for the behavior of IgG bound on a SpA affinity column, and alterations in the affinity of the ligands for IgG-Fab clearly affected the conditions for eluting the bound IgG. Thus, a histidine-scanning library combined with a structure-based design was shown to be effective in engineering novel pH-sensitive proteins.
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Affiliation(s)
- Masayuki Tsukamoto
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan ; Manufacturing Technology Association of Biologics, Chuo-ku, Kobe, Japan
| | - Hideki Watanabe
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST), Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Ayako Ooishi
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST), Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Shinya Honda
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan ; Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST), Higashi, Tsukuba, Ibaraki 305-8566, Japan ; Manufacturing Technology Association of Biologics, Chuo-ku, Kobe, Japan
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10
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Haghpanah JS, Tu R, Da Silva S, Yan D, Mueller S, Weder C, Foster EJ, Sacui I, Gilman JW, Montclare JK. Bionanocomposites: Differential Effects of Cellulose Nanocrystals on Protein Diblock Copolymers. Biomacromolecules 2013; 14:4360-7. [DOI: 10.1021/bm401304w] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Jennifer S. Haghpanah
- Department
of Chemical and Biomolecular Engineering, Polytechnic Institute of New York University, Brooklyn, New York 11201, United States
| | - Raymond Tu
- Department
of Chemical Engineering, City College of New York, New York, New York 10031, United States
| | - Sandra Da Silva
- Biomaterials
and Biosystems Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Deng Yan
- Skirball
Institute of Biomolecular Medicine, Microscopy Core Facilities, NYU Medical Center, New York, New York, 10016, United States
| | - Silvana Mueller
- Adolphe
Merkle Institute, University of Fribourg, CH-1723 Marly, Switzerland
| | - Christoph Weder
- Adolphe
Merkle Institute, University of Fribourg, CH-1723 Marly, Switzerland
| | - E. Johan Foster
- Adolphe
Merkle Institute, University of Fribourg, CH-1723 Marly, Switzerland
| | - Iulia Sacui
- Materials
Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Jeffery W. Gilman
- Materials
Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Jin Kim Montclare
- Department
of Chemical and Biomolecular Engineering, Polytechnic Institute of New York University, Brooklyn, New York 11201, United States
- Department
of Biochemistry, SUNY Downstate Medical Center, Brooklyn, New York 11203, United States
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11
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Bu L, Crowley MF, Himmel ME, Beckham GT. Computational investigation of the pH dependence of loop flexibility and catalytic function in glycoside hydrolases. J Biol Chem 2013; 288:12175-86. [PMID: 23504310 DOI: 10.1074/jbc.m113.462465] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellulase enzymes cleave glycosidic bonds in cellulose to produce cellobiose via either retaining or inverting hydrolysis mechanisms, which are significantly pH-dependent. Many fungal cellulases function optimally at pH ~5, and their activities decrease dramatically at higher or lower pH. To understand the molecular-level implications of pH in cellulase structure, we use a hybrid, solvent-based, constant pH molecular dynamics method combined with pH-based replica exchange to determine the pK(a) values of titratable residues of a glycoside hydrolase (GH) family 6 cellobiohydrolase (Cel6A) and a GH family 7 cellobiohydrolase (Cel7A) from the fungus Hypocrea jecorina. For both enzymes, we demonstrate that a bound substrate significantly affects the pKa values of the acid residues at the catalytic center. The calculated pK(a) values of catalytic residues confirm their proposed roles from structural studies and are consistent with the experimentally measured apparent pKa values. Additionally, GHs are known to impart a strained pucker conformation in carbohydrate substrates in active sites for catalysis, and results from free energy calculations combined with constant pH molecular dynamics suggest that the correct ring pucker is stable near the optimal pH for both Cel6A and Cel7A. Much longer molecular dynamics simulations of Cel6A and Cel7A with fixed protonation states based on the calculated pK(a) values suggest that pH affects the flexibility of tunnel loops, which likely affects processivity and substrate complexation. Taken together, this work demonstrates several molecular-level effects of pH on GH enzymes important for cellulose turnover in the biosphere and relevant to biomass conversion processes.
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Affiliation(s)
- Lintao Bu
- National Bioenergy Center, Colorado School of Mines, Golden, Colorado 80401, USA.
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12
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Genetic engineering in biomimetic composites. Trends Biotechnol 2012; 30:191-7. [DOI: 10.1016/j.tibtech.2012.01.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 01/02/2012] [Accepted: 01/03/2012] [Indexed: 11/22/2022]
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13
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Caparrós C, Lant N, Smets J, Cavaco-Paulo A. Effects of adsorption properties and mechanical agitation of two detergent cellulases towards cotton cellulose. BIOCATAL BIOTRANSFOR 2012. [DOI: 10.3109/10242422.2012.666840] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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14
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Murtaugh ML, Fanning SW, Sharma TM, Terry AM, Horn JR. A combinatorial histidine scanning library approach to engineer highly pH-dependent protein switches. Protein Sci 2011; 20:1619-31. [PMID: 21766385 DOI: 10.1002/pro.696] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 07/07/2011] [Indexed: 12/17/2022]
Abstract
There is growing interest in the development of protein switches, which are proteins whose function, such as binding a target molecule, can be modulated through environmental triggers. Efforts to engineer highly pH sensitive protein-protein interactions typically rely on the rational introduction of ionizable groups in the protein interface. Such experiments are typically time intensive and often sacrifice the protein's affinity at the permissive pH. The underlying thermodynamics of proton-linkage dictate that the presence of multiple ionizable groups, which undergo a pK(a) change on protein binding, are necessary to result in highly pH-dependent binding. To test this hypothesis, a novel combinatorial histidine library was developed where every possible combination of histidine and wild-type residue is sampled throughout the interface of a model anti-RNase A single domain VHH antibody. Antibodies were coselected for high-affinity binding and pH-sensitivity using an in vitro, dual-function selection strategy. The resulting antibodies retained near wild-type affinity yet became highly sensitive to small decreases in pH, drastically decreasing their binding affinity, due to the incorporation of multiple histidine groups. Several trends were observed, such as histidine "hot-spots," which will help enhance the development of pH switch proteins as well as increase our understanding of the role of ionizable residues in protein interfaces. Overall, the combinatorial approach is rapid, general, and robust and should be capable of producing highly pH-sensitive protein affinity reagents for a number of different applications.
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Affiliation(s)
- Megan L Murtaugh
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
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15
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Nozaki K, Nishijima H, Arai T, Mizuno M, Sato N, Amano Y. Regulation of Adsorption Behavior of Carbohydrate-Binding Module Family 1 and Endo-β-1,4-Glucanase onto Crystalline Cellulose. J Appl Glycosci (1999) 2011. [DOI: 10.5458/jag.jag.jag-2011_007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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16
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du Plessis L, Rose SH, van Zyl WH. Exploring improved endoglucanase expression in Saccharomyces cerevisiae strains. Appl Microbiol Biotechnol 2009; 86:1503-11. [PMID: 20041241 DOI: 10.1007/s00253-009-2403-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 12/05/2009] [Accepted: 12/06/2009] [Indexed: 10/20/2022]
Abstract
The endoglucanase I and II genes (egI or Cel7B and egII or Cel5A) of Trichoderma reesei QM6a were successfully cloned and expressed in Saccharomyces cerevisiae under the transcriptional control of the yeast ENO1 promoter and terminator sequences. Random mutagenesis of the egI-bearing plasmid resulted in a twofold increase in extracellular EGI activity. Both endoglucanase genes were co-expressed with the synthetic, codon-optimised cellobiohydrolase gene (s-cbhI) from T. reesei as well as the beta-glucosidase gene (bgl1) from Saccharomycopsis fibuligera in S. cerevisiae. Extracellular endoglucanase activity was lower when co-expressed with s-cbhI or bgl1. Recombinant strains were able to hydrolyse phosphoric acid swollen cellulose, generating mainly cellotriose, cellobiose and glucose. Cellobiose accumulated, suggesting the beta-glucosidase activity to be the rate-limiting factor. As a consequence, the recombinant strains were unable to produce enough glucose for growth on amorphous cellulose. The results of this study provide insight into further optimisation of recombinantly expressed cellulase combinations for saccharification and fermentation of cellulose to ethanol.
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Affiliation(s)
- Lisa du Plessis
- Department of Microbiology, University of Stellenbosch, De Beer Street, Stellenbosch, 7600, South Africa
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17
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Watanabe H, Matsumaru H, Ooishi A, Feng Y, Odahara T, Suto K, Honda S. Optimizing pH response of affinity between protein G and IgG Fc: how electrostatic modulations affect protein-protein interactions. J Biol Chem 2009; 284:12373-83. [PMID: 19269963 PMCID: PMC2673305 DOI: 10.1074/jbc.m809236200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 02/23/2009] [Indexed: 01/11/2023] Open
Abstract
Protein-protein interaction in response to environmental conditions enables sophisticated biological and biotechnological processes. Aiming toward the rational design of a pH-sensitive protein-protein interaction, we engineered pH-sensitive mutants of streptococcal protein G B1, a binder to the IgG constant region. We systematically introduced histidine residues into the binding interface to cause electrostatic repulsion on the basis of a rigid body model. Exquisite pH sensitivity of this interaction was confirmed by surface plasmon resonance and affinity chromatography employing a clinically used human IgG. The pH-sensitive mechanism of the interaction was analyzed and evaluated from kinetic, thermodynamic, and structural viewpoints. Histidine-mediated electrostatic repulsion resulted in significant loss of exothermic heat of the binding that decreased the affinity only at acidic conditions, thereby improving the pH sensitivity. The reduced binding energy was partly recovered by "enthalpy-entropy compensation." Crystal structures of the designed mutants confirmed the validity of the rigid body model on which the effective electrostatic repulsion was based. Moreover, our data suggested that the entropy gain involved exclusion of water molecules solvated in a space formed by the introduced histidine and adjacent tryptophan residue. Our findings concerning the mechanism of histidine-introduced interactions will provide a guideline for the rational design of pH-sensitive protein-protein recognition.
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Affiliation(s)
- Hideki Watanabe
- National Institute of Advanced Industrial Science and Technology, Central 6, Tsukuba 305-8566, Japan
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18
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Lavan LM, Van Dyk JS, Chan H, Doi RH, Pletschke BI. Effect of physical conditions and chemicals on the binding of a mini-CbpA from Clostridium cellulovorans to a semi-crystalline cellulose ligand. Lett Appl Microbiol 2009; 48:419-25. [PMID: 19187497 DOI: 10.1111/j.1472-765x.2008.02545.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS To investigate the effect that environmental factors have on Clostridium cellulovorans cellulose binding domain (CBD) binding to a semi-crystalline cellulose ligand, namely Avicel. METHODS AND RESULTS The behaviour of a 58 kDa mini-CbpA protein containing the CBD from the scaffoldin protein of C. cellulovorans was studied in the presence of various environmental factors, in order to determine whether such factors promote or reduce CBD binding to its ligand, thus potentially affecting its activity on the substrate. The amount of binding was found to be dependent on the Avicel concentration and optimal binding occurred when the ligand concentration was 15 mg ml(-1). Optimal CBD binding occurred at pH 7.0 and at an incubation temperature of 28 degrees C. The effects of dithiothreitol (DTT), 2-mercaptoethanol, acetone, butanol, ethanol and butyric acid were also investigated. CONCLUSIONS Temperature, pH, DTT, 2-mercaptoethanol and solvents were shown to affect the binding of C. cellulovorans CBD to Avicel. SIGNIFICANCE AND IMPACT OF THE STUDY Clostridium cellulovorans CBD binding to Avicel is affected by physical conditions and chemicals.
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Affiliation(s)
- L M Lavan
- Department of Biochemistry, Microbiology and Biotechnology, Rhodes University, Grahamstown, South Africa
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19
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Ahola S, Turon X, Osterberg M, Laine J, Rojas OJ. Enzymatic hydrolysis of native cellulose nanofibrils and other cellulose model films: effect of surface structure. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:11592-9. [PMID: 18778090 DOI: 10.1021/la801550j] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Model films of native cellulose nanofibrils, which contain both crystalline cellulose I and amorphous domains, were used to investigate the dynamics and activities of cellulase enzymes. The enzyme binding and degradation of nanofibril films were compared with those for other films of cellulose, namely, Langmuir-Schaefer and spin-coated regenerated cellulose, as well as cellulose nanocrystal cast films. Quartz crystal microbalance with dissipation (QCM-D) was used to monitor the changes in frequency and energy dissipation during incubation at varying enzyme concentrations and experimental temperatures. Structural and morphological changes of the cellulose films upon incubation with enzymes were evaluated by using atomic force microscopy. The QCM-D results revealed that the rate of enzymatic degradation of the nanofibril films was much faster compared to the other types of cellulosic films. Higher enzyme loads did not dramatically increase the already fast degradation rate. Real-time measurements of the coupled contributions of enzyme binding and hydrolytic reactions were fitted to an empirical model that closely described the cellulase activities. The hydrolytic potential of the cellulase mixture was found to be considerably affected by the nature of the substrates, especially their crystallinity and morphology. The implications of these observations are discussed in this report.
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Affiliation(s)
- S Ahola
- Department of Forest Products Technology, Faculty of Chemistry and Materials Sciences, Helsinki University of Technology, P.O. Box 3320, FIN-02015 TKK, Espoo, Finland
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20
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Shoseyov O, Shani Z, Levy I. Carbohydrate binding modules: biochemical properties and novel applications. Microbiol Mol Biol Rev 2006; 70:283-95. [PMID: 16760304 PMCID: PMC1489539 DOI: 10.1128/mmbr.00028-05] [Citation(s) in RCA: 351] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Polysaccharide-degrading microorganisms express a repertoire of hydrolytic enzymes that act in synergy on plant cell wall and other natural polysaccharides to elicit the degradation of often-recalcitrant substrates. These enzymes, particularly those that hydrolyze cellulose and hemicellulose, have a complex molecular architecture comprising discrete modules which are normally joined by relatively unstructured linker sequences. This structure is typically comprised of a catalytic module and one or more carbohydrate binding modules (CBMs) that bind to the polysaccharide. CBMs, by bringing the biocatalyst into intimate and prolonged association with its substrate, allow and promote catalysis. Based on their properties, CBMs are grouped into 43 families that display substantial variation in substrate specificity, along with other properties that make them a gold mine for biotechnologists who seek natural molecular "Velcro" for diverse and unusual applications. In this article, we review recent progress in the field of CBMs and provide an up-to-date summary of the latest developments in CBM applications.
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Affiliation(s)
- Oded Shoseyov
- The Institute of Plant Science and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 76100, Israel.
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21
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Chen H, Bernstein BW, Sneider JM, Boyle JA, Minamide LS, Bamburg JR. In Vitro Activity Differences between Proteins of the ADF/Cofilin Family Define Two Distinct Subgroups†. Biochemistry 2004; 43:7127-42. [PMID: 15170350 DOI: 10.1021/bi049797n] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The actin depolymerizing factor (ADF)/cofilins are an essential group of proteins that are important regulators of actin filament turnover in vivo. Although protists and yeasts express only a single member of this family, metazoans express two or more members in many cell types. In cells expressing both ADF and cofilin, differences have been reported in the regulation of their expression, their pH sensitivity, and their intracellular distribution. Each member has qualitatively similar interactions with actin, but quantitative differences have been noted. Here we compared quantitative differences between chick ADF and chick cofilin using several assays that measure G-actin binding, actin filament length distribution, and assembly/disassembly dynamics. Quantitative differences were measured in the critical concentrations of the complexes required for assembly, in the effects of nucleotide and divalent metal on actin monomer binding, in pH-dependent severing, in enhancement of filament minus end off-rates, and in steady-state filament length distributions generated in similar mixtures. Some of these assays were used to compare the activities of several ADF/cofilins from across phylogeny, most of which fall into one of two groups based upon their behavior. The ADF-like group has higher affinities for Mg(2+)-ATP-G-actin than the cofilin-like group and a greater pH-dependent depolymerizing activity.
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Affiliation(s)
- Hui Chen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA
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22
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Abstract
Many researchers have acknowledged the fact that there exists an immense potential for the application of the cellulose-binding domains (CBDs) in the field of biotechnology. This becomes apparent when the phrase "cellulose-binding domain" is used as the key word for a computerized patent search; more then 150 hits are retrieved. Cellulose is an ideal matrix for large-scale affinity purification procedures. This chemically inert matrix has excellent physical properties as well as low affinity for nonspecific protein binding. It is available in a diverse range of forms and sizes, is pharmaceutically safe, and relatively inexpensive. Present studies into the application of CBDs in industry have established that they can be applied in the modification of physical and chemical properties of composite materials and the development of modified materials with improved properties. In agro-biotechnology, CBDs can be used to modify polysaccharide materials both in vivo and in vitro. The CBDs exert nonhydrolytic fiber disruption on cellulose-containing materials. The potential applications of "CBD technology" range from modulating the architecture of individual cells to the modification of an entire organism. Expressing these genes under specific promoters and using appropriate trafficking signals, can be used to alter the nutritional value and texture of agricultural crops and their final products.
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Affiliation(s)
- Ilan Levy
- Institute of Plant Science and Genetics in Agriculture and Otto Warburg Centre for Agricultural Biotechnology, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, PO Box 12, Rehovot 76100, Israel
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Gusakov AV, Sinitsyn AP, Markov AV, Sinitsyna OA, Ankudimova NV, Berlin AG. Study of protein adsorption on indigo particles confirms the existence of enzyme--indigo interaction sites in cellulase molecules. J Biotechnol 2001; 87:83-90. [PMID: 11267701 DOI: 10.1016/s0168-1656(01)00234-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Adsorption of several crude and purified cellulases (from Trichoderma reesei, Penicillium verruculosum and Chrysosporium lucknowense) on indigo particles and Avicel cellulose was studied. Much higher amounts of protein were bound to indigo than to cellulose under similar conditions. For different purified enzymes, the quantity of bound protein per mg of adsorbent (indigo or cellulose) varied in the range of 57-111 and 0-62 microg x mg(-1), respectively. However, in general, the enzyme adsorption on indigo was less specific than the adsorption on cellulose. Three endoglucanases, having the highest indigo-binding ability, demonstrated the best washing performance in the process of enzymatic denim treatment. These data confirmed our previous findings that certain cellulases, which have indigo-binding sites (clusters of closely located aromatic and other non-polar residues) on the surface of their molecules, may remove indigo from the denim fabric better than cellulases with lower content of hydrophobic residues exposed to solvent.
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Affiliation(s)
- A V Gusakov
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119899, Moscow, Russia
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Lehtiö J, Wernérus H, Samuelson P, Teeri TT, Ståhl S. Directed immobilization of recombinant staphylococci on cotton fibers by functional display of a fungal cellulose-binding domain. FEMS Microbiol Lett 2001; 195:197-204. [PMID: 11179652 DOI: 10.1111/j.1574-6968.2001.tb10521.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The immobilization of recombinant staphylococci onto cellulose fibers through surface display of a fungal cellulose-binding domain (CBD) was investigated. Chimeric proteins containing the CBD from Trichoderma reesei cellulase Cel6A were found to be correctly targeted to the cell wall of Staphylococcus carnosus cells, since full-length proteins could be extracted and affinity-purified. Furthermore, surface accessibility of the CBD was verified using a monoclonal antibody and functionality in terms of cellulose-binding was demonstrated in two different assays in which recombinant staphylococci were found to efficiently bind to cotton fibers. The implications of this strategy of directed immobilization for the generation of whole-cell microbial tools for different applications will be discussed.
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Affiliation(s)
- J Lehtiö
- Department of Biotechnology, Royal Institute of Technology (KTH), SE-100 44 Stockholm, Sweden
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25
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Surface hydrophobic amino acid residues in cellulase molecules as a structural factor responsible for their high denim-washing performance. Enzyme Microb Technol 2000; 27:664-671. [PMID: 11064048 DOI: 10.1016/s0141-0229(00)00264-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The denim-washing performance of six purified fungal cellulases (four endo-1,4-beta-D-glucanases and two cellobiohydrolases) was compared using a model microassay. The performance of cellobiohydrolases per mg of protein was much lower than that of endoglucanases. For endoglucanases, it varied up to 5 times between the best and the worst enzyme. Experiments with amino acids immobilized on cross-linked agarose showed that their side chains may bind indigo owing to hydrophobic interactions and formation of hydrogen bonds. The best binding effects provided Tyr and Phe. Analysis of three-dimensional structures of cellulase molecules showed that a certain correlation exists between the washing performance of enzyme and (i) quantity (percentage) of aromatic residues exposed to solvent on the surface of protein globule or (ii) overall percentage of the surface hydrophobic residues. Data presented provide an evidence that the molecules of certain cellulases, which have hydrophobic domains (clusters of closely located non-polar residues) on their surface, may bind indigo and thus act as emulsifiers helping the dye to float out of cellulose fibers to the bulk solution.
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Brun E, Johnson PE, Creagh AL, Tomme P, Webster P, Haynes CA, McIntosh LP. Structure and binding specificity of the second N-terminal cellulose-binding domain from Cellulomonas fimi endoglucanase C. Biochemistry 2000; 39:2445-58. [PMID: 10704194 DOI: 10.1021/bi992079u] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 1,4-beta-glucanase CenC from Cellulomonas fimi contains two cellulose-binding domains, CBD(N1) and CBD(N2), arranged in tandem at its N-terminus. These homologous CBDs are distinct in their selectivity for binding amorphous and not crystalline cellulose. Multidimensional heteronuclear nuclear magnetic resonance (NMR) spectroscopy was used to determine the tertiary structure of CBD(N2) in the presence of saturating amounts of cellopentaose. A total of 1996 experimental restraints were used to calculate an ensemble of 21 final structures for the protein. CBD(Nu2) is composed of 11 beta-strands, folded into two antiparallel beta-sheets, with a topology of a jellyroll beta-sandwich. On the basis of patterns of chemical shift perturbations accompanying the addition of cellooligosaccharides, as well as the observation of intermolecular protein-sugar NOE interactions, the cellulose-binding site of CBD(N2) was identified as a cleft that lies across one face of the beta-sandwich. The thermodynamic basis for the binding of cellooligosaccharides was investigated using isothermal titration calorimetry and NMR spectroscopy. Binding is enthalpically driven and consistent with a structural model involving hydrogen bonding between the equatorial hydroxyls of the glucopyranosyl rings and polar amino acid side chains lining the CBD(N2) cleft. Affinity electrophoresis was used to determine that CBD(N2) also binds soluble beta-1,4-linked polymers of glucose, including hydroxyethylcellulose and beta-1,3-1,4-glucans. This study complements a previous analysis of CBD(N1) [Johnson, P. E., Joshi, M. D., Tomme, P., Kilburn, D. G., and McIntosh, L. P. (1996) Biochemistry 35, 14381-14394] and demonstrates that the homologous CBDs from CenC share very similar structures and sugar binding properties.
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Affiliation(s)
- E Brun
- Protein Engineering Network of Centres of Excellence, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, Canada
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